I am trying to reproduce this kind of figure (Chemokines differentially regulated in the five differents cells type on top) :
I would like to do the same, first with just M1 and M2 conditions, and eventually more. I would also like to be able to choose the genes in this heatmap (if you have advises on how to do this, I'll take it !)
So for now I have :
- the AffyBatch form the CEL files
- the annotated expression set normalized with rma().
- The MarrayLM from lmfit(data.rma,design)
- The MarrayLM from eBayes(data.fit) with pair-wise comparisons (contrasts)
From which one should I build the matrix for heatmap() ? How ?
I want to focus on gene coding for plasma membrane proteins, is there a way to do this ?
Thanks for your help !