Question about False Discovery Rate in AltAnalyze

[dicty]

Hi,

I'm trying to use AltAnalyze for Exon Array analysis, but didn't find
how to define False Discovery Rate (FDR) or q-value in the analysis
parameters settings. I'm not familiar with AltAnalyze and may miss
something.

Could anyone tell me how to setup FDR in the AltAnalyze for Exon Array
analysis?

Thanks a lot!

Dicty

[Nathan Salomonis]

Hi Dicty,

AltAnalyze various algorithms are discussed in more detail here:
http://www.altanalyze.org/help.htm#algorithm_description

For exon array gene expression analyses, BH adjusted p-values of the 1-way ANOVA rawp is provided. For alternative exon analyses, no adjusted p is provided for MiDAS (run using the included Affymetrix Power Tools) and no adjusted p-value for the splicing-index or FIRMA associated p-values. Adding a BH adjusted p for the splicing-index or FIRMA analysis could be added to the next version if you believe this would be of particularly useful.

Best,
Nathan

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