[BioC] Extracting topTable data from saved file

[Ekta Jain]

Hi Avoks,
The toptable is generated from your fit object. In LIMMA, you would need an object for the Venn Diagram function (http://127.0.0.1:22029/library/limma/html/venn.html) this in your case should be a vennCounts or decideTests(fit). 

But if you do not have access to your fit object and only have the toptable, then what you could do is read your toptables data in separate vectors or dataframes. Intersect() and merge() can give you common genes BUT between 2 vectors only. 

Intersect2() can apparently work on more than two vectors http://cran.r-project.org/web/packages/MergeGUI/MergeGUI.pdf. 

These can give you a start. You could read more on the same functions as well.


HTH,
Ekta


-----Original Message-----
From: Ovokeraye Achinike-Oduaran [mailto:ovokeraye at gmail.com] 
Sent: 15 May 2012 12:21
To: Ekta Jain
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Extracting topTable data from saved file

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.

-Avoks




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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