[BioC] LIMMA decideTests result zero from contrast matrix

[Steve Lianoglou]

Hi,

First order of business: please don't cross post between mailing list
-- it's generally considered bad etiquette.

Second:

On Fri, May 4, 2012 at 2:44 AM, Ekta Jain <Ekta_Jain at jubilantbiosys.com> wrote:
> Dear All,
> I am using the LIMMA package to create 2 contrasts for my data and then calculating the vennCounts of the decideTests from the contrast.fit to be able to create venn Diagrams.
>
> The code works fine but the summary(results) shows zeros for all i.e. no gene were up regulated or downregulated. This is not true for my data since toptable output shows Log fold change greater than > 2.

What are the adjusted p-values for these genes?

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact