Hi, suppose I have an experiment where I compare Drug A to control however I do this experiment with 3 cell lines. Lets say I run an RNA.seq on this and PCA analysis shows a clear separation of cell lines but within each cell line, Drug and control separates out nicely. The question is should I run the the analysis separately for each cell line and take the intersection OR should I run it all in the same model but correcting for cell line? For example using limma it would look something like this.
design <- model.matrix(~0+ key$group + key$cell )
the header would look something like this:
control druga cell1 cell2
and the makeContrasts(pn=drug1-control , levels=design)
if I do take this method how would I define my contrast to see the DGE for all three cell lines seperately?
Or should I just do the analysis separately for each cell line and then take the intersection of the DGE from each cellline?
so in summary its a two part question.
1. should I run the model together or separately?
2. and if I run it together how do I define my contrast so that I find the DGE for each cell separately. Say I want to find DGE only in cell3?
thanks in advance!