[BioC] help needed with the design matrix
Nair [guest]
guest at bioconductor.org
Wed Apr 16 21:13:15 CEST 2014
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 )
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:
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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