[BioC] edgeR: topTags
li.wang at ttu.edu
Tue May 29 17:18:01 CEST 2012
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.
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,
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
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"
Thank you very much for your time and help.
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