Hi KJ Lim, Once you have your row names of interest i.e up-regulated or down- regulated genes you can easily fetch other information for those row names. For instance the results from limma link back to samples by heatmaps. A heat map of upregulated genes: >expVal<-(eset[geneList,]) # Assuming eset if the expression set, it will take all columns for row names matching the geneList >heatmap(expVal) # this will create the heat map In a similar way you can create matrix of genes and logFC etc and then fetch data or also follow what Li suggested – output entire limma resuls to excel sheet and then sort on logFC. Most commonly used threshold is logFC >=2 for upregulated and logFC>=-2 for downregulated genes. Kindly note that summary(decideTests(lrt)) uses a different logFC cut off to call genes upregulated and or downregulated. This cut off i think is logFC >=0 and logFC <=0 for upregulated and downregulated respectively. Best, Ekta From: KJ Lim [mailto:jinkeanlim@gmail.com] Sent: 31 May 2012 11:54 To: Ekta Jain; Wang, Li Cc: Bioconductor mailing list Subject: Re: [BioC] edgeR: topTags 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<mailto: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=""> [mailto: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<mailto:bioconductor- bounces@r-project.org=""> [bioconductor-bounces@r-project.org<mailto :bioconductor-bounces@r-project.org="">] On Behalf Of KJ Lim [jinkeanlim@gmail.com<mailto: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<mailto: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<mailto: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. 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Dear Ekta, Thanks for your replied and guide. :) Best regards, KJ Lim On 1 June 2012 09:41, Ekta Jain <ekta_jain@jubilantbiosys.com> wrote: > Hi KJ Lim,**** > > Once you have your row names of interest i.e up-regulated or > down-regulated genes you can easily fetch other information for those row > names. For instance the results from limma link back to samples by > heatmaps. A heat map of upregulated genes:**** > > >expVal<-(eset[geneList,])**** > > # Assuming eset if the expression set, it will take all columns for row > names matching the geneList**** > > >heatmap(expVal)**** > > # this will create the heat map**** > > ** ** > > In a similar way you can create matrix of genes and logFC etc and then > fetch data or also follow what Li suggested – output entire limma resuls to > excel sheet and then sort on logFC. Most commonly used threshold is logFC > >=2 for upregulated and logFC>=-2 for downregulated genes.**** > > ** ** > > Kindly note that summary(decideTests(lrt)) uses a different logFC cut off > to call genes upregulated and or downregulated. This cut off i think is > logFC >=0 and logFC <=0 for upregulated and downregulated respectively.*** > * > > ** ** > > Best,**** > > Ekta**** > > ** ** > > ** ** > > ** ** > > *From:* KJ Lim [mailto:jinkeanlim@gmail.com] > *Sent:* 31 May 2012 11:54 > *To:* Ekta Jain; Wang, Li > *Cc:* Bioconductor mailing list > > *Subject:* Re: [BioC] edgeR: topTags**** > > ** ** > > 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**** > > ** ** > 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]]