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Error: collinearity in combined matrix of intercept and covariates for model 0 #21
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Hi Abhishek
could you please tell me what the contents of mat1.txt are?
Thanks
Ernest
… On 7 Feb 2017, at 12:22, abhisheksinghnl ***@***.***> wrote:
Hi,
I am running mmdiff, with three groups each with 3 replicates. The program throws up this error:
The command that I am using is :
~/Softwares/MMseq/mmseq/bin/mmdiff-linux -m mat1.txt /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_3.namesorted.bam.hits.gene.mmseq > E18vsOthers.mmdiff
and this is what happens:
Min unique hits fraction for normalisation: 1
No. threads: 16
Parsing /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_3.namesorted.bam.hits.gene.mmseq
Analysing 32637 features
Using 12943/32637 features for normalisation.
Log scale normalisation factors:
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_1.namesorted.bam.hits.gene.mmseq -0.0922577
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_2.namesorted.bam.hits.gene.mmseq 0.157586
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_3.namesorted.bam.hits.gene.mmseq -0.309913
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_1.namesorted.bam.hits.gene.mmseq 0.370167
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_2.namesorted.bam.hits.gene.mmseq 0.127327
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_3.namesorted.bam.hits.gene.mmseq -0.515323
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_1.namesorted.bam.hits.gene.mmseq 0.04334
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_2.namesorted.bam.hits.gene.mmseq 0.1999
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_3.namesorted.bam.hits.gene.mmseq 0.153414
Design matrix for model 0 ([1|M]):
Error: collinearity in combined matrix of intercept and covariates for model 0
Could you please let me know, how to fix this.
Thank you
Best regards
Abhishek
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Hi,
here is the content of mat1.txt file
## matrices_file1:
# M; no. of rows = no. of observations
1 0 0
1 0 0
1 0 0
0 1 0
0 1 0
0 1 0
0 0 1
0 0 1
0 0 1
# C; no. of rows = no. of observations and no. of columns = 2 (one for each
model)
0 0
0 0
0 0
0 1
0 1
0 1
0 1
0 1
0 1
# P0(collapsed); no. of rows = no. of classes for model 0
1
# P1(collapsed); no. of rows = no. of classes for model 1
.5
-.5
On Fri, Feb 10, 2017 at 3:40 PM, Ernest Turro <notifications@github.com>
wrote:
… Hi Abhishek
could you please tell me what the contents of mat1.txt are?
Thanks
Ernest
> On 7 Feb 2017, at 12:22, abhisheksinghnl ***@***.***>
wrote:
>
> Hi,
>
> I am running mmdiff, with three groups each with 3 replicates. The
program throws up this error:
>
> The command that I am using is :
>
> ~/Softwares/MMseq/mmseq/bin/mmdiff-linux -m mat1.txt
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
E18_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
Rat/Ageing/AlignedBowtie1/E18/E18_2.namesorted.bam.hits.gene.mmseq
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
E18_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
Rat/Ageing/AlignedBowtie1/P1/P1_1.namesorted.bam.hits.gene.mmseq
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
P1_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
Rat/Ageing/AlignedBowtie1/P1/P1_3.namesorted.bam.hits.gene.mmseq
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
P3_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
Rat/Ageing/AlignedBowtie1/P3/P3_2.namesorted.bam.hits.gene.mmseq
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
P3_3.namesorted.bam.hits.gene.mmseq > E18vsOthers.mmdiff
> and this is what happens:
>
> Min unique hits fraction for normalisation: 1
> No. threads: 16
> Parsing /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
E18_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
Rat/Ageing/AlignedBowtie1/E18/E18_2.namesorted.bam.hits.gene.mmseq
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
E18_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
Rat/Ageing/AlignedBowtie1/P1/P1_1.namesorted.bam.hits.gene.mmseq
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
P1_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
Rat/Ageing/AlignedBowtie1/P1/P1_3.namesorted.bam.hits.gene.mmseq
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
P3_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
Rat/Ageing/AlignedBowtie1/P3/P3_2.namesorted.bam.hits.gene.mmseq
/media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
P3_3.namesorted.bam.hits.gene.mmseq
> Analysing 32637 features
> Using 12943/32637 features for normalisation.
> Log scale normalisation factors:
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
E18_1.namesorted.bam.hits.gene.mmseq -0.0922577
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
E18_2.namesorted.bam.hits.gene.mmseq 0.157586
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
E18_3.namesorted.bam.hits.gene.mmseq -0.309913
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
P1_1.namesorted.bam.hits.gene.mmseq 0.370167
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
P1_2.namesorted.bam.hits.gene.mmseq 0.127327
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
P1_3.namesorted.bam.hits.gene.mmseq -0.515323
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
P3_1.namesorted.bam.hits.gene.mmseq 0.04334
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
P3_2.namesorted.bam.hits.gene.mmseq 0.1999
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
P3_3.namesorted.bam.hits.gene.mmseq 0.153414
> Design matrix for model 0 ([1|M]):
> Error: collinearity in combined matrix of intercept and covariates for
model 0
>
>
> Could you please let me know, how to fix this.
>
> Thank you
>
> Best regards
> Abhishek
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
>
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Hi,
If you're just comparing a model with a common mean to one with three means, you can do mmdiff -de 3 3 3. That's the easiest thing, and it is equivalent to a slightly expanded version (with an extra replicate in the third condition) of the example on the github readme:
https://raw.githubusercontent.com/eturro/mmseq/master/doc/332.mat
bw
Ernest
… On 10 Feb 2017, at 15:20, abhisheksinghnl ***@***.***> wrote:
Hi,
here is the content of mat1.txt file
## matrices_file1:
# M; no. of rows = no. of observations
1 0 0
1 0 0
1 0 0
0 1 0
0 1 0
0 1 0
0 0 1
0 0 1
0 0 1
# C; no. of rows = no. of observations and no. of columns = 2 (one for each
model)
0 0
0 0
0 0
0 1
0 1
0 1
0 1
0 1
0 1
# P0(collapsed); no. of rows = no. of classes for model 0
1
# P1(collapsed); no. of rows = no. of classes for model 1
.5
-.5
On Fri, Feb 10, 2017 at 3:40 PM, Ernest Turro ***@***.***>
wrote:
> Hi Abhishek
>
> could you please tell me what the contents of mat1.txt are?
>
> Thanks
> Ernest
>
> > On 7 Feb 2017, at 12:22, abhisheksinghnl ***@***.***>
> wrote:
> >
> > Hi,
> >
> > I am running mmdiff, with three groups each with 3 replicates. The
> program throws up this error:
> >
> > The command that I am using is :
> >
> > ~/Softwares/MMseq/mmseq/bin/mmdiff-linux -m mat1.txt
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
> E18_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
> Rat/Ageing/AlignedBowtie1/E18/E18_2.namesorted.bam.hits.gene.mmseq
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
> E18_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
> Rat/Ageing/AlignedBowtie1/P1/P1_1.namesorted.bam.hits.gene.mmseq
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
> P1_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
> Rat/Ageing/AlignedBowtie1/P1/P1_3.namesorted.bam.hits.gene.mmseq
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
> P3_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
> Rat/Ageing/AlignedBowtie1/P3/P3_2.namesorted.bam.hits.gene.mmseq
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
> P3_3.namesorted.bam.hits.gene.mmseq > E18vsOthers.mmdiff
> > and this is what happens:
> >
> > Min unique hits fraction for normalisation: 1
> > No. threads: 16
> > Parsing /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
> E18_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
> Rat/Ageing/AlignedBowtie1/E18/E18_2.namesorted.bam.hits.gene.mmseq
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
> E18_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
> Rat/Ageing/AlignedBowtie1/P1/P1_1.namesorted.bam.hits.gene.mmseq
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
> P1_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
> Rat/Ageing/AlignedBowtie1/P1/P1_3.namesorted.bam.hits.gene.mmseq
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
> P3_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/
> Rat/Ageing/AlignedBowtie1/P3/P3_2.namesorted.bam.hits.gene.mmseq
> /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
> P3_3.namesorted.bam.hits.gene.mmseq
> > Analysing 32637 features
> > Using 12943/32637 features for normalisation.
> > Log scale normalisation factors:
> > /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
> E18_1.namesorted.bam.hits.gene.mmseq -0.0922577
> > /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
> E18_2.namesorted.bam.hits.gene.mmseq 0.157586
> > /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/
> E18_3.namesorted.bam.hits.gene.mmseq -0.309913
> > /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
> P1_1.namesorted.bam.hits.gene.mmseq 0.370167
> > /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
> P1_2.namesorted.bam.hits.gene.mmseq 0.127327
> > /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/
> P1_3.namesorted.bam.hits.gene.mmseq -0.515323
> > /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
> P3_1.namesorted.bam.hits.gene.mmseq 0.04334
> > /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
> P3_2.namesorted.bam.hits.gene.mmseq 0.1999
> > /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/
> P3_3.namesorted.bam.hits.gene.mmseq 0.153414
> > Design matrix for model 0 ([1|M]):
> > Error: collinearity in combined matrix of intercept and covariates for
> model 0
> >
> >
> > Could you please let me know, how to fix this.
> >
> > Thank you
> >
> > Best regards
> > Abhishek
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub, or mute the thread.
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#21 (comment)>, or mute
> the thread
> <https://github.com/notifications/unsubscribe-auth/AUAA5xDoWVFfZ6fOvShTwtJe3XyUp2YAks5rbHbAgaJpZM4L5a7B>
> .
>
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Hi,
I am running mmdiff, with three groups each with 3 replicates. The program throws up this error:
The command that I am using is :
~/Softwares/MMseq/mmseq/bin/mmdiff-linux -m mat1.txt /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/E18/E18_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P1/P1_3.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_1.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_2.namesorted.bam.hits.gene.mmseq /media/data/u0106457/FASTQ/Rat/Ageing/AlignedBowtie1/P3/P3_3.namesorted.bam.hits.gene.mmseq > E18vsOthers.mmdiff
and this is what happens:
Could you please let me know, how to fix this.
Thank you
Best regards
Abhishek
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