[BioC] Extracting topTable data from saved file

Ekta Jain Ekta_Jain at jubilantbiosys.com
Tue May 15 06:03:44 CEST 2012

Hi Avoks,
What you are looking for is the decideTests(). Assuming 'fit' is your LIMMA fit object, something like:
> Results <- decideTests(fit)
# gives you counts of upregulated(1) and downregulated(-1) genes in each comparison. Kindly note that default cut-off for LogFC =0, this can be changed
> summary(Results) 
> vennDiagram(Results)
# You can pull out commonly upregulated gene lists by doing
geneList<-which(Results[,1] == 1 & results[,2] == 1)
# and commonly downregulated by changing 1 to -1 above

Hope this helps,

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Ovokeraye Achinike-Oduaran
Sent: 15 May 2012 08:26
To: bioconductor at r-project.org
Subject: [BioC] Extracting topTable data from saved file

Hi all, 

I have a few topTables saved from my Limma analyses of a number of studies. I would like to know what genes are common to groups of these tables, what genes are unique to each table and eventually draw a Venn diagram if possible. Any suggestions will be greatly appreciated. 



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