[BioC] adjusted p values of the genes in the intersection of Venn

[Margaret Gardiner-Garden]

Dear Benjamin, Thanks for your thoughts.
You are right that the hypothesis for each gene in the intersection would be
the gene is affected by both treatments.  However, we cannot merge the
groups into treated versus nontreated because the increase in expression
with treatment A is generally higher than that for treatment B ie they are
not equivalent treatments.

Regards
Marg
-----Original Message-----
From: Benjamin Otto [mailto:b.otto at uke.uni-hamburg.de] 
Sent: Wednesday, 15 November 2006 11:38 PM
To: 'Margaret Gardiner-Garden'; bioconductor at stat.math.ethz.ch
Subject: AW: [BioC] adjusted p values of the genes in the intersection of
Venn

Hi Margaret,

I'm not quite sure if one can "merge" some FDR values.
What hypothesis would you want the new FDR to stand for? Something like "is
the gene affected by both treatments.."? How about merging the four groups
(treatment A, treatment A reference, treatment B, treatment B reference) to
two newer ones (treated, non-treated) and look what FDR values these genes
get?  Please correct me if I misunderstood your question. :)

Regards
Benjamin

-----Ursprüngliche Nachricht-----
Von: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Margaret
Gardiner-Garden
Gesendet: 15 November 2006 06:07
An: bioconductor at stat.math.ethz.ch
Betreff: [BioC] adjusted p values of the genes in the intersection of Venn

Hi,  We have two lists of genes (one regulated by treatment A and the other
regulated by treatment B ).  Each list contains genes with a BY adjusted p
value (or FDR) <0.01.  As we expected from the biology, when we do a Venn
diagram many of the genes that are affected by treatment A are also affected
by treatment B ie lie in the intersection.  We are wondering how to
calculate the FDR of the intersection set.  If the gene belongs to both
sets, does this mean that its FDR is now less than 0.01? And does this then
mean that the genes that are not in the intersection set (ie are exclusive
to treatment A or treatment B) have a FDR more than 0.01?

 

We would really appreciate any advice that people can give...

 

Thanks in advance,

Marg

 

Dr Margaret Gardiner-Garden

Garvan Institute of Medical Research

384 Victoria Street

Darlinghurst Sydney

NSW 2010 Australia

 

Phone: 61 2 9295 8348

Fax: 61 2 9295 8321

 

 


	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor