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Using MapMan

Overrepresentation Analysis

Overrepresentation Analysis
Answer
3/4/15 5:43 PM
Hi all,
I used pageman to do the functional enrichment analysis of my interested genes. The Pageman within mapman gives no significant bins, but the online pageman tool produces many significant bins. So, what's the differences between these two and which one should I rely on?

Which test and multiple test correction method are being used in the online pageman ORA tool?


struggled for several days and couldn't find answers.

Thanks in advance!

RE: Overrepresentation Analysis
Answer
3/4/15 6:12 PM as a reply to dong li.
Hi

the online tool uses Fisher's exact test and NO correction, instead at the bottom it gives you significance thresholds which you can use to check which values are significant. If the FDR threshold is smaller than any of the realized p-values, than indeed you would have no signicant p-values in the online toll either.

Otherwise a common problem in the Java PageMan is that ALL genes (changing and background) need to be loaded and the significant need to be flagged or be above a FC threshold.

Björn

RE: Overrepresentation Analysis
Answer
3/4/15 6:29 PM as a reply to Björn Usadel.
Hi Björn,

thanks for your quick reply.

I noticed the values at the bottom, something like this: 0.0020022488889188715Bonferoni 0.000140056022408964

the second value is the threshold for Bonferoni correction, am i right? how about the first one?

Another difference I noticed is that the online tool only need the gene list. The one within mapman also needs the data column.

I'm new to mapman, so based on your experiences, which tool do you recommend?

Thanks