I have an RNA-seq experiments with a control, and 4 treatments, for each I have 3 replicates. I would like to find genes that are differentially expressed in any of these conditions compared to the control samples.
Meaning if gene A is up/down-regulated in one or more of the treatments compared to the control, I would like to know about it.
lcd = read.delim('mydata', row.names=1, as.is=T) group = factor(c(rep("ctrl", 3), rep("treat1",3), rep("treat2",3), rep("treat3",3),rep("treat4",3))) cds <- DGEList(lcd, group = group)
What is the alternative for using exactTest multiple times and intersecting the results, given that I would not like to average the expression of the treatments as the different treatment have different consequences?