[BioC] help needed with the design matrix
James W. MacDonald
jmacdon at uw.edu
Wed Apr 16 21:21:41 CEST 2014
You will have to give more information than that.
On 4/16/2014 3:13 PM, Nair [guest] wrote:
> Hi All,
> I am in the process of performing a DE of the RNA-seq data.
> I have "paired" experimental design for a "treatment".In addition to this, I have 4 categorical explanatory variables. I am aiming to look for DE genes upon "treatment" which might be dependent upon these categorical variables. The design I used:
> design<-model.matrix(~treat+pair+var1+var2, data=x )
This looks like you have only two categorical explanatory variables. It
would help if you gave more information about the number of samples you
have, and the different treatments.
> When I tried to run "estimateGLMCommonDisp" using this design, I am getting the following error.
> Error in glmFit.default(y, design = design, dispersion = dispersion, offset = offset, :
> Design matrix not of full rank. The following coefficients not estimable:
This means that you have either too many parameters for the number of
samples, or one (or more) of your variables are linear combinations of
the other variables. Unless you show what you are doing, nobody will be
able to say much more than that.
> Do you have any idea about a correct design matrix for this kind of setting in edgeR ?
> Thanks a lot
> -- output of sessionInfo():
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
>  LC_CTYPE=fi_FI.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>  LC_MONETARY=fi_FI.UTF-8 LC_MESSAGES=en_GB.UTF-8
>  LC_PAPER=en_GB.UTF-8 LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  grid stats graphics grDevices utils datasets methods
>  base
> other attached packages:
>  lattice_0.20-29 gplots_2.13.0 VennDiagram_1.6.5 edgeR_3.4.2
>  limma_3.18.13
> loaded via a namespace (and not attached):
>  bitops_1.0-6 caTools_1.16 gdata_2.13.3 gtools_3.3.1
>  KernSmooth_2.23-12
> Sent via the guest posting facility at bioconductor.org.
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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