[BioC] LIMMA decideTests result zero from contrast matrix

[Ekta Jain]

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

-Ekta

-----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

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
The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email.
www.jubl.com