I'm trying to reproduce the analysis done in this paper and I've tried R's siggenes and Tmev, but I don't get the same list of differentially-expressed genes using both methods, even when tuning the delta parameter, nor do I get the two genes (RPV1 and IFI30) he picked for qPCR from any of my lists of differentially-expressed genes. I'm pretty sure I chose the wrong samples. I tried two-class unpaired SAM, for control vs. chron's disease, but even that doesn't include the genes he chose. I also tried multiclass SAM, still no good.
The author used such samples:
GSM's: normal, crohn's disease, ulcerative colitis, infectious colitis, indeterminate colitis
Then he grouped them as:
control, unaffected and affected (Note: the affected/ unaffected come from the fact that data were taken from symptomatic vs asymptomatic patients having the diseases)
Do I use multiclass or two-class SAM: "control vs affected" or "control vs unaffected" or "affected vs unaffected".
In the paper he said he used healthy vs diseased.. Grateful if someone could enlighten me.
I'm going to try the options meanwhile.