Error: collinearity in combined matrix of intercept and covariates for model 0

[abhisheksinghnl]

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

[eturro]

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.

[abhisheksinghnl]

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. > — 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> .

[eturro]

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> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.