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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > The information contained in this electronic message and in any > attachments to this message is confidential, legally privileged and > intended only for use by the person or entity to which this electronic > message is addressed. If you are not the intended recipient, and have > received this message in error, please notify the sender and system manager > by return email and delete the message and its attachments and also you are > hereby notified that any distribution, copying, review, retransmission, > dissemination or other use of this electronic transmission or the > information contained in it is strictly prohibited. Please note that any > views or opinions presented in this email are solely those of the author > and may not represent those of the Company or bind the Company. Any > commitments made over e-mail are not financially binding on the company > unless accompanied or followed by a valid purchase order. This message has > been scanned for viruses and dangerous content by Mail Scanner, and is > believed to be clean. The Company accepts no liability for any damage > caused by any virus transmitted by this email. > www.jubl.com > > [[alternative HTML version deleted]]