[BioC] edgeR: topTags

[Ekta Jain]

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 at r-project.org [mailto:bioconductor-bounces at 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 at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of KJ Lim [jinkeanlim at 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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