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Haplotype, isoform and gene level expression analysis using multi-mapping RNA-seq reads
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Error: collinearity in combined matrix of intercept and covariates for model 0 #21

Open abhisheksinghnl opened 7 years ago

abhisheksinghnl commented 7 years ago

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 commented 7 years ago

Hi Abhishek

could you please tell me what the contents of mat1.txt are?

Thanks Ernest

On 7 Feb 2017, at 12:22, abhisheksinghnl notifications@github.com 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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abhisheksinghnl commented 7 years ago

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 notifications@github.com 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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eturro commented 7 years ago

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 notifications@github.com 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 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 notifications@github.com 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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