I'm analyzing a microarray data and stuck at the design matrix command.
I have few samples, in which I divided them into two groups i.e. "Controls" & "Diseased".
I assigned the samples information as a factor with two levels "C" & "D".
In what exact order should I assign the levels? If I assign levels as C, D then I get the logFC value as say X and if I do it as D, C I get the logFC value as -X.
Should I start with the diseased group (D) or control group (C)?
In default, in what exact order the design matrix take the levels?
My code is as follows:
# ^^^ Which one should I consider first in the above command? The diseased group or control group? ^^^
contr.str <- c()
for(i in 1:(len-1))contr.str<-c(contr.str, paste(lev[(i+1):len], lev[i], sep="-"))
top <- topTable(fit2, number=nrow(fit2), adjust.method="fdr")
Thanks in advance