[BioC] LIMMA decideTests result zero from contrast matrix

Ekta Jain Ekta_Jain at jubilantbiosys.com
Mon May 7 05:38:12 CEST 2012

Hi Steve,
What do you mean by "cross-post between mailing list" ? I usually mail to both Bioconductor and R to avoid the suggestion to email the 'correct' place. More so since i was not sure who would be better able to answer my question.

Adjusted p-values are pretty bad - 0.999540865122392


-----Original Message-----
From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] 
Sent: 04 May 2012 19:18
To: Ekta Jain
Cc: bioconductor at r-project.org
Subject: Re: [BioC] LIMMA decideTests result zero from contrast matrix


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


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 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
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