[BioC] Extracting topTable data from saved file

Ovokeraye Achinike-Oduaran ovokeraye at gmail.com
Tue May 15 08:50:48 CEST 2012

Thanks Ekta. I don't think that that's what I'm looking for though. I probably wasn't very clear with my question. I already have topTables meeting my set thresholds from different studies relating to a certain condition saved on my comp. So, what I'm looking to do now is to call on these saved text files to get a list of genes common across, say, tables 1,2 &3 (an intersect). As well as a list of unique genes per table (3 lists) and perhaps, a Venn diagram capturing the data from the 3 tables(1 Venn diagram with 3 circles). But thanks again.


On 15 May 2012, at 6:03 AM, Ekta Jain <Ekta_Jain at jubilantbiosys.com> wrote:

> 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,
> Ekta
> -----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. 
> Thanks.
> -Avoks
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