[BioC] help needed with the design matrix

[James W. MacDonald]

Hi Nair,

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.

Best,

Jim


>
>
> Do you have any idea about a correct design matrix for this kind of setting in edgeR ?
>
> Thanks a lot
> Nair
>
>   -- output of sessionInfo():
>
>
>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=fi_FI.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=fi_FI.UTF-8    LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] lattice_0.20-29   gplots_2.13.0     VennDiagram_1.6.5 edgeR_3.4.2
> [5] limma_3.18.13
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-6       caTools_1.16       gdata_2.13.3       gtools_3.3.1
> [5] KernSmooth_2.23-12
>
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099