Loss of probes during preprocessIllumina #188
Comments
|
This sounds pretty weird. Could you should the output from mini 1.30?
…On Wed, Jul 3, 2019 at 8:20 AM LambertDorssers ***@***.***> wrote:
I have been using minfi 1.28.4 until recently which returns me approx 860K
of probes after preprocessIllimina of EPIC arrays. This is used as input
for the conumee copy number package.
Now I have updated to minfi 1.30.0, preprocessIllumina returns only about
670K probes for the same set of EPIC arrays.
I do not find an explanation for this difference anywhere and I wonder
what has been changed in the software causing this difference and whether
this change should provide me better quality output? I am not a developer,
but a regular user of the minfi package.
Many thanks,
Lambert Dorssers
ErasmusMC Rotterdam
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Dear Kasper,
Indeed it is weird.
Below I will show the description of the relevant files as genereated in the process.
Minfi1.28 generated.
rgSet_epic
class: RGChannelSet
dim: 1051539 121
metadata(0):
assays(2): Green Red
rownames(1051539): 1600101 1600111 ... 99810990 99810992
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ... 203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
mset_epic_Illu
class: MethylSet
dim: 865859 121
metadata(0):
assays(2): Meth Unmeth
rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ... 203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
Preprocessing
Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 1
minfi version: 1.28.4
Manifest version: 0.3.0
Next I have run the above shown RG file with preprocessIllumina from minfi 1.30
mset_epic_Illu<-preprocessIllumina(rgSet_epic, bg.correct = T, normalize = "controls", reference=31)
mset_epic_Illu
class: MethylSet
dim: 865859 121
metadata(0):
assays(2): Meth Unmeth
rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ... 203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
Preprocessing
Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 31
minfi version: 1.30.0
Manifest version: 0.3.0
This appears to be identical, to my surprise.
Next I reloaded yesterdays RData file
load("~/userData/Methyl/AllEpicCCBC20190702.RData")
Rgset generated using:
rgSet_epic <- read.metharray.exp(base="./Data/Epic",targets = TarEpic[1:121,], force = TRUE)
rgSet_epic
class: RGChannelSet
dim: 851151 121
metadata(0):
assays(2): Green Red
rownames(851151): 1600101 1600111 ... 85626239 85626241
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ... 203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
mset_epic_Illu
class: MethylSet
dim: 678455 121
metadata(0):
assays(2): Meth Unmeth
rownames(678455): cg09835024 cg14361672 ... cg14585103 cg10633746
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ... 203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
Preprocessing
Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 31
minfi version: 1.30.0
Manifest version: 0.3.0
It appears that the Rgset has lost many probes.
So if there is a problem, it seems to happen during loading of the data with read.metharray.exp and not during preprocessing!
I hope this clarifies the issue.
Sorry for making an interpretation error, but something is not going OK
Bets Lambert
…--------------------------------------
Lambert CJ Dorssers, PhD
Dept of Pathology, JNI, BE 435a
Erasmus MC Rotterdam,
Bezoekadres: Wytemaweg 80, 3015 CN Rotterdam
P.O. Box 2040, 3000 CA, Rotterdam
Netherlands.
Phone: +31-10-7044378/44332 / +31-6-12029131
Email: l.dorssers@erasmusmc.nl<mailto:l.dorssers@erasmusmc.nl>
---------------------------------------
From: Kasper Daniel Hansen [mailto:notifications@github.com]
Sent: Wednesday, July 3, 2019 10:43 AM
To: hansenlab/minfi
Cc: L.C.J. Dorssers; Author
Subject: Re: [hansenlab/minfi] Loss of probes during preprocessIllumina (#188)
This sounds pretty weird. Could you should the output from mini 1.30?
On Wed, Jul 3, 2019 at 8:20 AM LambertDorssers ***@***.***> wrote:
I have been using minfi 1.28.4 until recently which returns me approx 860K
of probes after preprocessIllimina of EPIC arrays. This is used as input
for the conumee copy number package.
Now I have updated to minfi 1.30.0, preprocessIllumina returns only about
670K probes for the same set of EPIC arrays.
I do not find an explanation for this difference anywhere and I wonder
what has been changed in the software causing this difference and whether
this change should provide me better quality output? I am not a developer,
but a regular user of the minfi package.
Many thanks,
Lambert Dorssers
ErasmusMC Rotterdam
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Best,
Kasper
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It is hard to know what is going on here, since you don't have an issue
when you try to reproduce it today.
The most simple explanation is that you have somehow removed CpGs from the
object prior to saving it. I know you think you didn't, but it is hard to
know. You could take 1 sample and do something like
commonNames = intersect(rownames(OBJECT1), rownames(OBJECT2))
plot(getMeth(OBJECT1)[commonNames, 1], getMeth(OBJECT2)[commonNames, 1]))
to see if the values are the same (instead of plotting you could also use
all.equal). I would expect it to be the same, which further suggests that
you somehow removed CpGs prior to saving it.
Best,
Kasper
On Wed, Jul 3, 2019 at 11:15 AM LambertDorssers <notifications@github.com>
wrote:
… Dear Kasper,
Indeed it is weird.
Below I will show the description of the relevant files as genereated in
the process.
Minfi1.28 generated.
> rgSet_epic
class: RGChannelSet
dim: 1051539 121
metadata(0):
assays(2): Green Red
rownames(1051539): 1600101 1600111 ... 99810990 99810992
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
> mset_epic_Illu
class: MethylSet
dim: 865859 121
metadata(0):
assays(2): Meth Unmeth
rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
Preprocessing
Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 1
minfi version: 1.28.4
Manifest version: 0.3.0
Next I have run the above shown RG file with preprocessIllumina from minfi
1.30
> mset_epic_Illu<-preprocessIllumina(rgSet_epic, bg.correct = T, normalize
= "controls", reference=31)
> mset_epic_Illu
class: MethylSet
dim: 865859 121
metadata(0):
assays(2): Meth Unmeth
rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
Preprocessing
Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 31
minfi version: 1.30.0
Manifest version: 0.3.0
This appears to be identical, to my surprise.
Next I reloaded yesterdays RData file
> load("~/userData/Methyl/AllEpicCCBC20190702.RData")
Rgset generated using:
rgSet_epic <- read.metharray.exp(base="./Data/Epic",targets =
TarEpic[1:121,], force = TRUE)
> rgSet_epic
class: RGChannelSet
dim: 851151 121
metadata(0):
assays(2): Green Red
rownames(851151): 1600101 1600111 ... 85626239 85626241
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
> mset_epic_Illu
class: MethylSet
dim: 678455 121
metadata(0):
assays(2): Meth Unmeth
rownames(678455): cg09835024 cg14361672 ... cg14585103 cg10633746
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
Preprocessing
Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 31
minfi version: 1.30.0
Manifest version: 0.3.0
It appears that the Rgset has lost many probes.
So if there is a problem, it seems to happen during loading of the data
with read.metharray.exp and not during preprocessing!
I hope this clarifies the issue.
Sorry for making an interpretation error, but something is not going OK
Bets Lambert
--------------------------------------
Lambert CJ Dorssers, PhD
Dept of Pathology, JNI, BE 435a
Erasmus MC Rotterdam,
Bezoekadres: Wytemaweg 80, 3015 CN Rotterdam
P.O. Box 2040, 3000 CA, Rotterdam
Netherlands.
Phone: +31-10-7044378/44332 / +31-6-12029131
Email: ***@***.******@***.***>
---------------------------------------
From: Kasper Daniel Hansen ***@***.***
Sent: Wednesday, July 3, 2019 10:43 AM
To: hansenlab/minfi
Cc: L.C.J. Dorssers; Author
Subject: Re: [hansenlab/minfi] Loss of probes during preprocessIllumina
(#188)
This sounds pretty weird. Could you should the output from mini 1.30?
On Wed, Jul 3, 2019 at 8:20 AM LambertDorssers ***@***.***>
wrote:
> I have been using minfi 1.28.4 until recently which returns me approx
860K
> of probes after preprocessIllimina of EPIC arrays. This is used as input
> for the conumee copy number package.
> Now I have updated to minfi 1.30.0, preprocessIllumina returns only
about
> 670K probes for the same set of EPIC arrays.
> I do not find an explanation for this difference anywhere and I wonder
> what has been changed in the software causing this difference and
whether
> this change should provide me better quality output? I am not a
developer,
> but a regular user of the minfi package.
>
> Many thanks,
> Lambert Dorssers
> ErasmusMC Rotterdam
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <
#188?email_source=notifications&email_token=ABF2DH4TUOCPK7YLF6HMBLDP5RAKHA5CNFSM4H5CJAMKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G5BOKNQ>,
> or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/ABF2DHZ5LOAXURB37UFLH4TP5RAKHANCNFSM4H5CJAMA>
> .
>
--
Best,
Kasper
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Attempt to include the example array failed due to the size limitation.
I will send them through Surffilesender, I hope the mail adress will work
Best Lambert
From: L.C.J. Dorssers
Sent: Wednesday, July 3, 2019 11:56 AM
To: 'hansenlab/minfi'
Subject: RE: [hansenlab/minfi] Loss of probes during preprocessIllumina (#188)
Dear Kasper,
When testing the import, I think the problem is that combining the early days EPIC arrays with more recent filesseem to cause the loss of the probes.
By testing all samples, I have mapped the problem to a particular batch (202135260105) of EPIC arrays. When I use these arrays solely in the import, I get the low number of probes imported.
When I run the complete batch without these arrays, I do get the normal number.
This did not happen when using minfi 1.28 version.
Using conumee, we have previously noted that the lay out of the EPIC array was changed in the process and caused trouble. This could be bypassed suing the github version of Martin Sill (install_github("mwsill/conumee", force=T)).
Apparently something has changed to minfi, as I run the old minfi script on the same data set yesterday.
I hope this pinpoints the problem soewhat more.
I will attach a single array from the particular trouble creating batch for you to test.
Many thanks,
Lambert
From: Kasper Daniel Hansen [mailto:notifications@github.com]
Sent: Wednesday, July 3, 2019 11:39 AM
To: hansenlab/minfi
Cc: L.C.J. Dorssers; Author
Subject: Re: [hansenlab/minfi] Loss of probes during preprocessIllumina (#188)
It is hard to know what is going on here, since you don't have an issue
when you try to reproduce it today.
The most simple explanation is that you have somehow removed CpGs from the
object prior to saving it. I know you think you didn't, but it is hard to
know. You could take 1 sample and do something like
commonNames = intersect(rownames(OBJECT1), rownames(OBJECT2))
plot(getMeth(OBJECT1)[commonNames, 1], getMeth(OBJECT2)[commonNames, 1]))
to see if the values are the same (instead of plotting you could also use
all.equal). I would expect it to be the same, which further suggests that
you somehow removed CpGs prior to saving it.
Best,
Kasper
On Wed, Jul 3, 2019 at 11:15 AM LambertDorssers <notifications@github.com>
wrote:
… Dear Kasper,
Indeed it is weird.
Below I will show the description of the relevant files as genereated in
the process.
Minfi1.28 generated.
> rgSet_epic
class: RGChannelSet
dim: 1051539 121
metadata(0):
assays(2): Green Red
rownames(1051539): 1600101 1600111 ... 99810990 99810992
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
> mset_epic_Illu
class: MethylSet
dim: 865859 121
metadata(0):
assays(2): Meth Unmeth
rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
Preprocessing
Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 1
minfi version: 1.28.4
Manifest version: 0.3.0
Next I have run the above shown RG file with preprocessIllumina from minfi
1.30
> mset_epic_Illu<-preprocessIllumina(rgSet_epic, bg.correct = T, normalize
= "controls", reference=31)
> mset_epic_Illu
class: MethylSet
dim: 865859 121
metadata(0):
assays(2): Meth Unmeth
rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
Preprocessing
Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 31
minfi version: 1.30.0
Manifest version: 0.3.0
This appears to be identical, to my surprise.
Next I reloaded yesterdays RData file
> load("~/userData/Methyl/AllEpicCCBC20190702.RData")
Rgset generated using:
rgSet_epic <- read.metharray.exp(base="./Data/Epic",targets =
TarEpic[1:121,], force = TRUE)
> rgSet_epic
class: RGChannelSet
dim: 851151 121
metadata(0):
assays(2): Green Red
rownames(851151): 1600101 1600111 ... 85626239 85626241
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
> mset_epic_Illu
class: MethylSet
dim: 678455 121
metadata(0):
assays(2): Meth Unmeth
rownames(678455): cg09835024 cg14361672 ... cg14585103 cg10633746
rowData names(0):
colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
203168670113_R08C01 203179340066_R02C01
colData names(25): Order SampleCode ... RunLab filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19
Preprocessing
Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 31
minfi version: 1.30.0
Manifest version: 0.3.0
It appears that the Rgset has lost many probes.
So if there is a problem, it seems to happen during loading of the data
with read.metharray.exp and not during preprocessing!
I hope this clarifies the issue.
Sorry for making an interpretation error, but something is not going OK
Bets Lambert
--------------------------------------
Lambert CJ Dorssers, PhD
Dept of Pathology, JNI, BE 435a
Erasmus MC Rotterdam,
Bezoekadres: Wytemaweg 80, 3015 CN Rotterdam
P.O. Box 2040, 3000 CA, Rotterdam
Netherlands.
Phone: +31-10-7044378/44332 / +31-6-12029131
Email: ***@***.******@***.***>
---------------------------------------
From: Kasper Daniel Hansen ***@***.***
Sent: Wednesday, July 3, 2019 10:43 AM
To: hansenlab/minfi
Cc: L.C.J. Dorssers; Author
Subject: Re: [hansenlab/minfi] Loss of probes during preprocessIllumina
(#188)
This sounds pretty weird. Could you should the output from mini 1.30?
On Wed, Jul 3, 2019 at 8:20 AM LambertDorssers ***@***.***>
wrote:
> I have been using minfi 1.28.4 until recently which returns me approx
860K
> of probes after preprocessIllimina of EPIC arrays. This is used as input
> for the conumee copy number package.
> Now I have updated to minfi 1.30.0, preprocessIllumina returns only
about
> 670K probes for the same set of EPIC arrays.
> I do not find an explanation for this difference anywhere and I wonder
> what has been changed in the software causing this difference and
whether
> this change should provide me better quality output? I am not a
developer,
> but a regular user of the minfi package.
>
> Many thanks,
> Lambert Dorssers
> ErasmusMC Rotterdam
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <
#188?email_source=notifications&email_token=ABF2DH4TUOCPK7YLF6HMBLDP5RAKHA5CNFSM4H5CJAMKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G5BOKNQ>,
> or mute the thread
> <
https://github.com/notifications/unsubscribe-auth/ABF2DHZ5LOAXURB37UFLH4TP5RAKHANCNFSM4H5CJAMA>
> .
>
--
Best,
Kasper
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This sounds like a real bug. Please send me some files and check that
reading in only those files reproduces the problem. It should then be a
(relatively) easy fix. However, in a few days I will be going offline with
no internet access for 4 days.
Best,
Kasper
On Wed, Jul 3, 2019 at 12:03 PM LambertDorssers <notifications@github.com>
wrote:
… Attempt to include the example array failed due to the size limitation.
I will send them through Surffilesender, I hope the mail adress will work
Best Lambert
From: L.C.J. Dorssers
Sent: Wednesday, July 3, 2019 11:56 AM
To: 'hansenlab/minfi'
Subject: RE: [hansenlab/minfi] Loss of probes during preprocessIllumina
(#188)
Dear Kasper,
When testing the import, I think the problem is that combining the early
days EPIC arrays with more recent filesseem to cause the loss of the
probes.
By testing all samples, I have mapped the problem to a particular batch
(202135260105) of EPIC arrays. When I use these arrays solely in the
import, I get the low number of probes imported.
When I run the complete batch without these arrays, I do get the normal
number.
This did not happen when using minfi 1.28 version.
Using conumee, we have previously noted that the lay out of the EPIC array
was changed in the process and caused trouble. This could be bypassed suing
the github version of Martin Sill (install_github("mwsill/conumee",
force=T)).
Apparently something has changed to minfi, as I run the old minfi script
on the same data set yesterday.
I hope this pinpoints the problem soewhat more.
I will attach a single array from the particular trouble creating batch
for you to test.
Many thanks,
Lambert
From: Kasper Daniel Hansen ***@***.***
Sent: Wednesday, July 3, 2019 11:39 AM
To: hansenlab/minfi
Cc: L.C.J. Dorssers; Author
Subject: Re: [hansenlab/minfi] Loss of probes during preprocessIllumina
(#188)
It is hard to know what is going on here, since you don't have an issue
when you try to reproduce it today.
The most simple explanation is that you have somehow removed CpGs from the
object prior to saving it. I know you think you didn't, but it is hard to
know. You could take 1 sample and do something like
commonNames = intersect(rownames(OBJECT1), rownames(OBJECT2))
plot(getMeth(OBJECT1)[commonNames, 1], getMeth(OBJECT2)[commonNames, 1]))
to see if the values are the same (instead of plotting you could also use
all.equal). I would expect it to be the same, which further suggests that
you somehow removed CpGs prior to saving it.
Best,
Kasper
On Wed, Jul 3, 2019 at 11:15 AM LambertDorssers ***@***.***>
wrote:
> Dear Kasper,
>
> Indeed it is weird.
> Below I will show the description of the relevant files as genereated in
> the process.
> Minfi1.28 generated.
> > rgSet_epic
> class: RGChannelSet
> dim: 1051539 121
> metadata(0):
> assays(2): Green Red
> rownames(1051539): 1600101 1600111 ... 99810990 99810992
> rowData names(0):
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
> colData names(25): Order SampleCode ... RunLab filenames
> Annotation
> array: IlluminaHumanMethylationEPIC
> annotation: ilm10b4.hg19
> > mset_epic_Illu
> class: MethylSet
> dim: 865859 121
> metadata(0):
> assays(2): Meth Unmeth
> rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
> rowData names(0):
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
> colData names(25): Order SampleCode ... RunLab filenames
> Annotation
> array: IlluminaHumanMethylationEPIC
> annotation: ilm10b4.hg19
> Preprocessing
> Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 1
> minfi version: 1.28.4
> Manifest version: 0.3.0
>
> Next I have run the above shown RG file with preprocessIllumina from
minfi
> 1.30
>
> > mset_epic_Illu<-preprocessIllumina(rgSet_epic, bg.correct = T,
normalize
> = "controls", reference=31)
>
> > mset_epic_Illu
>
> class: MethylSet
>
> dim: 865859 121
>
> metadata(0):
>
> assays(2): Meth Unmeth
>
> rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
>
> rowData names(0):
>
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
>
> colData names(25): Order SampleCode ... RunLab filenames
>
> Annotation
>
> array: IlluminaHumanMethylationEPIC
>
> annotation: ilm10b4.hg19
>
> Preprocessing
>
> Method: Illumina, bg.correct = TRUE, normalize = controls, reference =
31
>
> minfi version: 1.30.0
>
> Manifest version: 0.3.0
> This appears to be identical, to my surprise.
>
> Next I reloaded yesterdays RData file
>
>
>
> > load("~/userData/Methyl/AllEpicCCBC20190702.RData")
>
> Rgset generated using:
>
> rgSet_epic <- read.metharray.exp(base="./Data/Epic",targets =
> TarEpic[1:121,], force = TRUE)
>
> > rgSet_epic
>
> class: RGChannelSet
>
> dim: 851151 121
>
> metadata(0):
>
> assays(2): Green Red
>
> rownames(851151): 1600101 1600111 ... 85626239 85626241
>
> rowData names(0):
>
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
>
> colData names(25): Order SampleCode ... RunLab filenames
>
> Annotation
>
> array: IlluminaHumanMethylationEPIC
>
> annotation: ilm10b4.hg19
>
> > mset_epic_Illu
>
> class: MethylSet
>
> dim: 678455 121
>
> metadata(0):
>
> assays(2): Meth Unmeth
>
> rownames(678455): cg09835024 cg14361672 ... cg14585103 cg10633746
>
> rowData names(0):
>
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
>
> colData names(25): Order SampleCode ... RunLab filenames
>
> Annotation
>
> array: IlluminaHumanMethylationEPIC
>
> annotation: ilm10b4.hg19
>
> Preprocessing
>
> Method: Illumina, bg.correct = TRUE, normalize = controls, reference =
31
>
> minfi version: 1.30.0
>
> Manifest version: 0.3.0
>
>
>
> It appears that the Rgset has lost many probes.
>
> So if there is a problem, it seems to happen during loading of the data
> with read.metharray.exp and not during preprocessing!
>
> I hope this clarifies the issue.
> Sorry for making an interpretation error, but something is not going OK
>
> Bets Lambert
>
> --------------------------------------
> Lambert CJ Dorssers, PhD
> Dept of Pathology, JNI, BE 435a
> Erasmus MC Rotterdam,
> Bezoekadres: Wytemaweg 80, 3015 CN Rotterdam
> P.O. Box 2040, 3000 CA, Rotterdam
> Netherlands.
> Phone: +31-10-7044378/44332 / +31-6-12029131
> Email: ***@***.******@***.***>
> ---------------------------------------
>
>
>
> From: Kasper Daniel Hansen ***@***.***
> Sent: Wednesday, July 3, 2019 10:43 AM
> To: hansenlab/minfi
> Cc: L.C.J. Dorssers; Author
> Subject: Re: [hansenlab/minfi] Loss of probes during preprocessIllumina
> (#188)
>
> This sounds pretty weird. Could you should the output from mini 1.30?
>
> On Wed, Jul 3, 2019 at 8:20 AM LambertDorssers ***@***.***>
> wrote:
>
> > I have been using minfi 1.28.4 until recently which returns me approx
> 860K
> > of probes after preprocessIllimina of EPIC arrays. This is used as
input
> > for the conumee copy number package.
> > Now I have updated to minfi 1.30.0, preprocessIllumina returns only
> about
> > 670K probes for the same set of EPIC arrays.
> > I do not find an explanation for this difference anywhere and I wonder
> > what has been changed in the software causing this difference and
> whether
> > this change should provide me better quality output? I am not a
> developer,
> > but a regular user of the minfi package.
> >
> > Many thanks,
> > Lambert Dorssers
> > ErasmusMC Rotterdam
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub
> > <
>
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>
> > or mute the thread
> > <
>
https://github.com/notifications/unsubscribe-auth/ABF2DHZ5LOAXURB37UFLH4TP5RAKHANCNFSM4H5CJAMA>
>
> > .
> >
>
>
> --
> Best,
> Kasper
>
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub<
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--
Best,
Kasper
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Best,
Kasper
|
|
Dear Kasper,
Finally I found out that the error has been a copy error in the original data files, which I needed to do because of switching to another computer.
Apparently, something was wrong with one of the files in the set, causing the malfunction.
In conclusion, nothing was wrong with the minfi package.
Please remove my issue on the github site, since the error was mine.
Many thanks and once again sorry for the trouble.
Best wishes,
Lambert
From: Kasper Daniel Hansen [mailto:notifications@github.com]
Sent: Wednesday, July 3, 2019 12:21 PM
To: hansenlab/minfi
Cc: L.C.J. Dorssers; Author
Subject: Re: [hansenlab/minfi] Loss of probes during preprocessIllumina (#188)
This sounds like a real bug. Please send me some files and check that
reading in only those files reproduces the problem. It should then be a
(relatively) easy fix. However, in a few days I will be going offline with
no internet access for 4 days.
Best,
Kasper
On Wed, Jul 3, 2019 at 12:03 PM LambertDorssers <notifications@github.com>
wrote:
… Attempt to include the example array failed due to the size limitation.
I will send them through Surffilesender, I hope the mail adress will work
Best Lambert
From: L.C.J. Dorssers
Sent: Wednesday, July 3, 2019 11:56 AM
To: 'hansenlab/minfi'
Subject: RE: [hansenlab/minfi] Loss of probes during preprocessIllumina
(#188)
Dear Kasper,
When testing the import, I think the problem is that combining the early
days EPIC arrays with more recent filesseem to cause the loss of the
probes.
By testing all samples, I have mapped the problem to a particular batch
(202135260105) of EPIC arrays. When I use these arrays solely in the
import, I get the low number of probes imported.
When I run the complete batch without these arrays, I do get the normal
number.
This did not happen when using minfi 1.28 version.
Using conumee, we have previously noted that the lay out of the EPIC array
was changed in the process and caused trouble. This could be bypassed suing
the github version of Martin Sill (install_github("mwsill/conumee",
force=T)).
Apparently something has changed to minfi, as I run the old minfi script
on the same data set yesterday.
I hope this pinpoints the problem soewhat more.
I will attach a single array from the particular trouble creating batch
for you to test.
Many thanks,
Lambert
From: Kasper Daniel Hansen ***@***.***
Sent: Wednesday, July 3, 2019 11:39 AM
To: hansenlab/minfi
Cc: L.C.J. Dorssers; Author
Subject: Re: [hansenlab/minfi] Loss of probes during preprocessIllumina
(#188)
It is hard to know what is going on here, since you don't have an issue
when you try to reproduce it today.
The most simple explanation is that you have somehow removed CpGs from the
object prior to saving it. I know you think you didn't, but it is hard to
know. You could take 1 sample and do something like
commonNames = intersect(rownames(OBJECT1), rownames(OBJECT2))
plot(getMeth(OBJECT1)[commonNames, 1], getMeth(OBJECT2)[commonNames, 1]))
to see if the values are the same (instead of plotting you could also use
all.equal). I would expect it to be the same, which further suggests that
you somehow removed CpGs prior to saving it.
Best,
Kasper
On Wed, Jul 3, 2019 at 11:15 AM LambertDorssers ***@***.***>
wrote:
> Dear Kasper,
>
> Indeed it is weird.
> Below I will show the description of the relevant files as genereated in
> the process.
> Minfi1.28 generated.
> > rgSet_epic
> class: RGChannelSet
> dim: 1051539 121
> metadata(0):
> assays(2): Green Red
> rownames(1051539): 1600101 1600111 ... 99810990 99810992
> rowData names(0):
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
> colData names(25): Order SampleCode ... RunLab filenames
> Annotation
> array: IlluminaHumanMethylationEPIC
> annotation: ilm10b4.hg19
> > mset_epic_Illu
> class: MethylSet
> dim: 865859 121
> metadata(0):
> assays(2): Meth Unmeth
> rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
> rowData names(0):
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
> colData names(25): Order SampleCode ... RunLab filenames
> Annotation
> array: IlluminaHumanMethylationEPIC
> annotation: ilm10b4.hg19
> Preprocessing
> Method: Illumina, bg.correct = TRUE, normalize = controls, reference = 1
> minfi version: 1.28.4
> Manifest version: 0.3.0
>
> Next I have run the above shown RG file with preprocessIllumina from
minfi
> 1.30
>
> > mset_epic_Illu<-preprocessIllumina(rgSet_epic, bg.correct = T,
normalize
> = "controls", reference=31)
>
> > mset_epic_Illu
>
> class: MethylSet
>
> dim: 865859 121
>
> metadata(0):
>
> assays(2): Meth Unmeth
>
> rownames(865859): cg18478105 cg09835024 ... cg10633746 cg12623625
>
> rowData names(0):
>
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
>
> colData names(25): Order SampleCode ... RunLab filenames
>
> Annotation
>
> array: IlluminaHumanMethylationEPIC
>
> annotation: ilm10b4.hg19
>
> Preprocessing
>
> Method: Illumina, bg.correct = TRUE, normalize = controls, reference =
31
>
> minfi version: 1.30.0
>
> Manifest version: 0.3.0
> This appears to be identical, to my surprise.
>
> Next I reloaded yesterdays RData file
>
>
>
> > load("~/userData/Methyl/AllEpicCCBC20190702.RData")
>
> Rgset generated using:
>
> rgSet_epic <- read.metharray.exp(base="./Data/Epic",targets =
> TarEpic[1:121,], force = TRUE)
>
> > rgSet_epic
>
> class: RGChannelSet
>
> dim: 851151 121
>
> metadata(0):
>
> assays(2): Green Red
>
> rownames(851151): 1600101 1600111 ... 85626239 85626241
>
> rowData names(0):
>
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
>
> colData names(25): Order SampleCode ... RunLab filenames
>
> Annotation
>
> array: IlluminaHumanMethylationEPIC
>
> annotation: ilm10b4.hg19
>
> > mset_epic_Illu
>
> class: MethylSet
>
> dim: 678455 121
>
> metadata(0):
>
> assays(2): Meth Unmeth
>
> rownames(678455): cg09835024 cg14361672 ... cg14585103 cg10633746
>
> rowData names(0):
>
> colnames(121): 201465910048_R02C01 201465910048_R03C01 ...
> 203168670113_R08C01 203179340066_R02C01
>
> colData names(25): Order SampleCode ... RunLab filenames
>
> Annotation
>
> array: IlluminaHumanMethylationEPIC
>
> annotation: ilm10b4.hg19
>
> Preprocessing
>
> Method: Illumina, bg.correct = TRUE, normalize = controls, reference =
31
>
> minfi version: 1.30.0
>
> Manifest version: 0.3.0
>
>
>
> It appears that the Rgset has lost many probes.
>
> So if there is a problem, it seems to happen during loading of the data
> with read.metharray.exp and not during preprocessing!
>
> I hope this clarifies the issue.
> Sorry for making an interpretation error, but something is not going OK
>
> Bets Lambert
>
> --------------------------------------
> Lambert CJ Dorssers, PhD
> Dept of Pathology, JNI, BE 435a
> Erasmus MC Rotterdam,
> Bezoekadres: Wytemaweg 80, 3015 CN Rotterdam
> P.O. Box 2040, 3000 CA, Rotterdam
> Netherlands.
> Phone: +31-10-7044378/44332 / +31-6-12029131
> Email: ***@***.******@***.***>
> ---------------------------------------
>
>
>
> From: Kasper Daniel Hansen ***@***.***
> Sent: Wednesday, July 3, 2019 10:43 AM
> To: hansenlab/minfi
> Cc: L.C.J. Dorssers; Author
> Subject: Re: [hansenlab/minfi] Loss of probes during preprocessIllumina
> (#188)
>
> This sounds pretty weird. Could you should the output from mini 1.30?
>
> On Wed, Jul 3, 2019 at 8:20 AM LambertDorssers ***@***.***>
> wrote:
>
> > I have been using minfi 1.28.4 until recently which returns me approx
> 860K
> > of probes after preprocessIllimina of EPIC arrays. This is used as
input
> > for the conumee copy number package.
> > Now I have updated to minfi 1.30.0, preprocessIllumina returns only
> about
> > 670K probes for the same set of EPIC arrays.
> > I do not find an explanation for this difference anywhere and I wonder
> > what has been changed in the software causing this difference and
> whether
> > this change should provide me better quality output? I am not a
> developer,
> > but a regular user of the minfi package.
> >
> > Many thanks,
> > Lambert Dorssers
> > ErasmusMC Rotterdam
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub
> > <
>
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> --
> Best,
> Kasper
>
>
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I have been using minfi 1.28.4 until recently which returns me approx 860K of probes after preprocessIllimina of EPIC arrays. This is used as input for the conumee copy number package.
Now I have updated to minfi 1.30.0, preprocessIllumina returns only about 670K probes for the same set of EPIC arrays.
I do not find an explanation for this difference anywhere and I wonder what has been changed in the software causing this difference and whether this change should provide me better quality output? I am not a developer, but a regular user of the minfi package.
Many thanks,
Lambert Dorssers
ErasmusMC Rotterdam
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