[BioC] Up & Downregulated genes using DESeq

[Ekta Jain]

Hi,
As far as i gather, the threshold for upregulated or downregulated genes should be >2FoldChange and >-2 FoldChange respectively. Not >0 or <0.

Best,
Ekta

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Omar Darwish
Sent: 27 March 2012 09:53
To: Steve Lianoglou
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Up & Downregulated genes using DESeq

Thanks Steve,

you are right (DownRegulated.txt + UpRegulated.txt == 2 * All.txt), So, you
are saying no need for the two lines of code to write (DownRegulated.txt
and UpRegulated.txt) and I can extract the Upregulated using (up <-
subset(resSig, foldChange > 0))   and the downregulated (down <-
subset(resSig, foldChange < 0)), right?

On Mon, Mar 26, 2012 at 11:09 PM, Steve Lianoglou <
mailinglist.honeypot at gmail.com> wrote:

> Hi,
>
> On Mon, Mar 26, 2012 at 10:59 PM, Omar Darwish <odarwish83 at gmail.com>
> wrote:
> > Hello All,
> >
> > I am using DESeq for identify differentially expressed genes among a
> couple
> > of samples. At the end of the calculations i write the results to 3 files
> > as follow:
> >
> > resSig <- res[ res$padj < .01, ]
> > write.table(resSig,"~DESeq\\All.txt")
> > write.table(resSig[ order( resSig$foldChange, -resSig$baseMean ), ]
> > ,"~\\DESeq\\DownRegulated.txt")
> > write.table(resSig[ order( -resSig$foldChange, -resSig$baseMean ),
> > ],"~\\DESeq\\UpRegulated.txt")
> >
> > My question here is,
> >
> >   - In the DESeq paper it is mentioned that the last two lines of code
> >   extracts the up and downregulated genes, So I'm thinking the sum of the
> >   number of genes in (DownRegulated.txt + UpRegulated.txt) should equals
> the
> >   number of genes with padj value < .01 in the file All.txt. But, that
> does
> >   not apply in my case as the numbers not even close. Any explanation or
> help
> >   is appreciated.
>
> I guess I must be missing something, but aren't the number of genes in
> your DownRegualted.txt file equal to the number of genes in your
> UpRegulated.txt file, which is also equal to the number of genes in
> your All.txt file? So, using your lingo:
>
> DownRegulated.txt + UpRegulated.txt == 2 * All.txt
>
> Right?
>
> You calls to `order(resSig$foldChange ...)` are just shuffling your
> rows around ... you're not removing any of them. If you want to split
> up and down regulated genes, you can perhaps subset rows that have
> foldChanges above (or below) zero, ie:
>
> up <- subset(resSig, foldChange > 0)
> write.table(up[order(up$foldChange, decreasing=TRUE),], "UpRegulated.txt")
>
> etc.
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
Regards,
Omar

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