Entering edit mode
Dear Eugene,
According to your design, Sample 31 is a unique treatment unto itself,
and
also a unique batch unto itself. Obviously it is impossible to
estimate
both the batch effect and the treatment effect from one sample. Hence
the
error message.
Best wishes
Gordon
> Date: Fri, 20 Dec 2013 16:49:43 -0800 (PST)
> From: "Eugene Bolotin [guest]" <guest at="" bioconductor.org="">
> To: bioconductor at r-project.org, elbolotin at gmail.com
> Subject: [BioC] EdgeR Design matrix not of full rank. The following
> coefficients not estimable erroR
>
>
> Hi I have the following samples:
> batch
> [1] 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 2055 1802
1802 2055
> [16] 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055
2055 1802 1802
> [31] 1157 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802
1802 2055 2055
> [46] 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055
> Levels: 1157 1802 2055
> treatment
> [1] TCGA-BR-6452 TCGA-BR-6453 tumor TCGA-BR-6454 tumor
> [6] TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 tumor TCGA-BR-6458
> [11] tumor TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-
BR-7196
> [16] TCGA-BR-7703 tumor TCGA-BR-7704 tumor TCGA-
BR-7707
> [21] TCGA-BR-7715 tumor TCGA-BR-7716 tumor TCGA-
BR-7717
> [26] tumor TCGA-BR-7723 TCGA-CD-5804 TCGA-CG-4437 TCGA-
CG-4441
> [31] TCGA-CG-4476 TCGA-CG-5716 TCGA-D7-6518 TCGA-D7-6519
TCGA-D7-6520
> [36] TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525
TCGA-D7-6526
> [41] TCGA-D7-6527 TCGA-D7-6528 TCGA-F1-6177 TCGA-F1-6875 TCGA-
FP-7735
> [46] tumor TCGA-FP-7829 tumor TCGA-HF-7131 TCGA-
HF-7132
> [51] TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-IN-7806 tumor
> 44 Levels: TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 ...
tumor
>
>
>
>
>
> I want to compare each sample from TCGA_X, to average mutant
background, I know it is possible, because I was able to do it using
standard commands.
> However, when I try to adjust for batch effects as follows:
> design=model.matrix(~batch+treatment)
> names(data.frame(design))
> group=treatment
> y=readDGE(files, path=wd, columns=c(1,2), group=group)
> #names(data.frame(design))
> design=model.matrix(~0+batch+treatment)
>
> names(data.frame(design))
> #rownames(design)=colnames(y)
> design
>
>> y = estimateGLMCommonDisp(y, design, verbose=TRUE)
> Error in glmFit.default(y, design = design, dispersion = dispersion,
offset = offset, :
> Design matrix not of full rank. The following coefficients not
estimable:
> treatmentTCGA-CG-4476
> as far as i can tell it is because the batch 1157 contains a normal
sample but does not contain any tumor samples.
> Is there a way around that?
> Thanks,
> Eugene
>
>
> -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] edgeR_3.4.2 limma_3.18.6
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.2
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
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