I have 130 individuals with their RNAseq data in 7 batches treated in a Case-Control study (Case=37 and Control=93). I would like to run differential gene expression analysis for 18258 genes for this study in Limma. When I read some discussions about removing batch effect in the model through Bioconductor's forum, I found that the best way to remove batch effect is to consider individuals as random in the model. So, regarding this assumption I created my design matrix as: (Patient=130; Treat: Yes=37 & No=93)
design = model.matrix(~Patient+Treat)
fit= lmFit(GenExp, design)
But, after I fitting the model and run in Limma, I got the following error:
Coefficients not estimable: TreatNo
Partial NA coefficients for 18258 probe(s)
How can I fix this issue? any other comments for removing batch effect? Thanks for any advise.