Error in preprocessQuantile and preprocessFunnorm

[michaelnoe]

I get an error while running preprocessFunnorm:
[preprocessFunnorm] Background and dye bias correction with noob
[preprocessFunnorm] Mapping to genome
[preprocessFunnorm] Quantile extraction
Error: number of cluster centres must lie between 1 and nrow(x)

and something similar for preprocessQuantile:
[preprocessQuantile] Mapping to genome.
Error: number of cluster centres must lie between 1 and nrow(x)

I only ran the basic code (no subsetting of the data like in the previous case):
targets <- read.metharray.sheet(getwd())
RGset <- read.metharray.exp(targets = targets)
mdata1 <- preprocessFunnorm(RGset)
mdata2<- preprocessQuantile(RGset)

[kasperdanielhansen]

How many samples, what is the sex distribution; print the `RGset` object and paste result here and finally what is R/minfi versions.

…

On Tue, Feb 5, 2019 at 12:19 PM michaelnoe ***@***.***> wrote: I get an error while running preprocessFunnorm: [preprocessFunnorm] Background and dye bias correction with noob [preprocessFunnorm] Mapping to genome [preprocessFunnorm] Quantile extraction Error: number of cluster centres must lie between 1 and nrow(x) and something similar for preprocessQuantile: [preprocessQuantile] Mapping to genome. Error: number of cluster centres must lie between 1 and nrow(x) I only ran the basic code (no subsetting of the data like in the previous case): 'targets <- read.metharray.sheet(getwd()) 'RGset <- read.metharray.exp(targets = targets) mdata1 <- preprocessFunnorm(RGset) mdata2<- preprocessQuantile(RGset) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#180>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEuhn7-_4ML7ULm3oEmPpz1IeBZW7p_Zks5vKb03gaJpZM4ajsGK> .

[michaelnoe]

It's two samples: 1 woman and 1 man:
the RGset is:
class: RGChannelSet
dim: 1051815 2
metadata(0):
assays(2): Green Red
rownames(1051815): 1600101 1600111 ... 99810990 99810992
rowData names(0):
colnames(2): 203219720041_R07C01 203219720041_R08C01
colData names(9): Sample_Name Sample_Well ... Basename filenames
Annotation
array: IlluminaHumanMethylationEPIC
annotation: ilm10b4.hg19

my setup:
platform x86_64-apple-darwin15.6.0
arch x86_64
os darwin15.6.0
system x86_64, darwin15.6.0
status
major 3
minor 5.2
year 2018
month 12
day 20
svn rev 75870
language R
version.string R version 3.5.2 (2018-12-20)
nickname Eggshell Igloo

minfi: version 1.28.3

[michaelnoe]

It's probably not associated with the setup, since I just tried it on the jhpce-cluster and it gives the same error...

[iranmdl]

I am having the same issue, any updates?

RGSet

class: RGChannelSet
dim: 622399 2
metadata(0):
assays(2): Green Red
rownames(622399): 10600313 10600322 ... 74810490 74810492
rowData names(0):
colnames(2): 5723646052_R02C02 5723646052_R04C01
colData names(13): Sample_Name Sample_Well ... Basename filenames
Annotation
  array: IlluminaHumanMethylation450k
  annotation: ilmn12.hg19

[RijndertAriese]

Hi,

I also encounter the same issue, could someone shed some light on this?

My RGSet:

class: RGChannelSet 
dim: 1051943 2 
metadata(0): 
assays(2): Green Red(1051943): 1600101 1600111 ... 99810990 99810992
rowData names(0):
colnames(2): BRO.Tumor BRO.Healthy
colData names(7): GSM_ID Sample_Name ... Basename filenames
Annotation
  array: IlluminaHumanMethylationEPIC
  annotation: ilm10b4.hg19

When I run preprocessQuantile(rgSet) I get Error: number of cluster centres must lie between 1 and nrow(x)

Any help would be appreciated