Question: How Was Sam (Microarray Analysis) Conducted In The Paper "Computational Repositioning Of The Anticonvulsant Topiramate For Inflammatory Bowel Disease"
3
gravatar for Olivier
5.8 years ago by
Olivier440
Olivier440 wrote:

Hello

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.

microarray sam • 1.7k views
ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 5.8 years ago by Olivier440

Did you try contacting the author?

ADD REPLYlink written 5.8 years ago by Devon Ryan90k

I'll try a bit more before. I thought that would be my last resort before contacting the author. But thanks anyways. Will do so if I don't manage.

ADD REPLYlink written 5.8 years ago by Olivier440

Link to the paper: http://www.ncbi.nlm.nih.gov/pubmed/21849664

ADD REPLYlink written 5.8 years ago by Istvan Albert ♦♦ 80k

I already have the paper, but there's no mention of how the samples were compared by SAM analysis.. I thought it would be easy, like comparing 2 samples.. I've done it like thus "control vs affected", "control vs unaffected" and "affected vs unaffected") with R, but I only managed to get only one of the mentioned genes (control vs affected, with a delta of 2.3; FDR 0.008; 10.7 false calls vs 489 called genes)..There's probably something I've missed..
Is multiclass comparison (haven't tried it yet) meaningful in this case. (I'm new to this kind of analysis, but it's so interesting) Thank you.

ADD REPLYlink written 5.8 years ago by Olivier440
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