Thanks Li for your input and thanks Ekta for your suggestion.

Using the command as suggested:
  >geneList<-which(de[,1] == 1)

The *geneList* will give me the row name of the up-regualted genes. May I
ask how can I get the values of logFC, LogCPM, LR,PValue,FDR show as well
for the *geneList*?

Thank you very much for you guys time and help.

Best regards,
KJ Lim


On 30 May 2012 07:52, Ekta Jain <Ekta_Jain@jubilantbiosys.com> wrote:

> Hi KJ Lim,
> To get the gene lists for up-regulated genes, you could try
> > geneList<-which(de[,1] == 1)
> ## if you have two contrasts
> > geneList<-which(de[,1] == 1 & de[,2] == 1)
>
> Changing '1' to '-1' will give down-regulated genes.
>
> Hope this helps.
>
> Best,
> Ekta
>
>
> -----Original Message-----
> From: bioconductor-bounces@r-project.org [mailto:
> bioconductor-bounces@r-project.org] On Behalf Of Wang, Li
> Sent: 29 May 2012 20:48
> To: KJ Lim; Bioconductor mailing list
> Subject: Re: [BioC] edgeR: topTags
>
> Hi,
>
> The second question, when giving the summary command,  the number after -1
> is the number of down-regulated genes and that after 1 is the up-regulated
> ones.
>
> The first question, when you export your top tags into tab delimited
> table, you can sort the table by logFC, the positive values of logFC
> corresponds to the up-regulated genes, while the negative values of logFC
> indicates the down-regulated genes.
>
> Hope that it is helpful.
>
> Cheers
> Li
> ________________________________________
> From: bioconductor-bounces@r-project.org [
> bioconductor-bounces@r-project.org] On Behalf Of KJ Lim [
> jinkeanlim@gmail.com]
> Sent: Tuesday, May 29, 2012 6:00 AM
> To: Bioconductor mailing list
> Subject: [BioC] edgeR: topTags
>
> Dear the edgeR community,
>
> Good day.
>
> 1.  Could someone please light me,  does the "topTags"  show also the
> down-regulated genes/tags in the top genes list? If it is not, how could I
> get
>     the down-regulated genes/tags list?
>
> 2.  Using this command:  summary(de <- decideTestsDGE(lrt))
>     is able to tell the total number of up-regulated and down-regulated
> genes/tags of the test. I would like to learn how can I extract these up
> and
>     down-regulated genes/tags list or I should look at the "topTags"
> command instead?
>
> Thank you very much for your time and help.
>
> Best regards,
> KJ Lim
>
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