

---- On Mon, 14 May 2012 23:50:48 -0700 Ovokeraye Achinike-Oduaran &lt;ovokeraye@gmail.com&gt; wrote ---- 


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 &amp;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. 


&gt;Yeah, I wanna know if there is a way to do it in R too cos I was doing comparison like this in excel by using advanced filtering to get unique genes and then matched between the lists. Guess it's not quite smart though..


Cheers,
Michelle

 
-Avoks 
 

 
 
 
On 15 May 2012, at 6:03 AM, Ekta Jain &lt;Ekta_Jain@jubilantbiosys.com&gt; wrote: 
 
&gt; Hi Avoks, 
&gt; What you are looking for is the decideTests(). Assuming 'fit' is your LIMMA fit object, something like: 
&gt;&gt; Results &lt;- decideTests(fit) 
&gt; # 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 
&gt;&gt; summary(Results) 
&gt;&gt; vennDiagram(Results) 
&gt; # You can pull out commonly upregulated gene lists by doing 
&gt; geneList&lt;-which(Results[,1] == 1 &amp; results[,2] == 1) 
&gt; # and commonly downregulated by changing 1 to -1 above 
&gt; 
&gt; Hope this helps, 
&gt; Ekta 
&gt; 
&gt; 
&gt; -----Original Message----- 
&gt; From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces@r-project.org] On Behalf Of Ovokeraye Achinike-Oduaran 
&gt; Sent: 15 May 2012 08:26 
&gt; To: bioconductor@r-project.org 
&gt; Subject: [BioC] Extracting topTable data from saved file 
&gt; 
&gt; Hi all, 
&gt; 
&gt; 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. 
&gt; 
&gt; Thanks. 
&gt; 
&gt; -Avoks 
&gt; 
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