I have three groups (A, B, C) to compare each with many samples: My goal is to normalize all groups as a whole and then get differential expression (DE) list for each pair.
My attempts so far with edgeR:
if i define my groups [
group <- c(rep("A",68),rep("B",65),rep("C",70)) ] before calcNormFactors and common estimateCommonDisp and exporting normalized values. It looks like normalization is occurring within each group (which i am not looking for)
what I tried is define entire samples as one group [ g
roup <- c(rep("A",203)) ] . I could get the normalized values: but my difficulty now it is not able to perform exactTest as group has only one entity.
After normalization I redefined the groups as in my first case still unable to perform the exactTest.
I really appreciate if you can suggest to over come this.... I am open to using other tools if they support this.