Hi Jenny, Thanks a lot. I appreciate your kind help. I really need to make efforts on learning R. Best Regards, Wang ----- Original Message ----- From: "Jenny Drnevich" <drnevich@illinois.edu> To: "Jixin Wang" <jixinwang at="" neo.tamu.edu="">, bioconductor at stat.math.ethz.ch Sent: Tuesday, November 4, 2008 12:55:22 PM GMT -06:00 US/Canada Central Subject: Re: [BioC] LIMMA Sort problem Hi Wang, In the newest version of limma (limma_2.16.2, which needs R 2.8.0), there is now a sort="none" option to topTable. Always check the help page for a function - ?topTable. HTH, Jenny At 11:17 AM 11/4/2008, Wang, Jixin wrote: >Dear All, I have one question about the >consistence between topTable output with GPR >file. In my GPR file, I have several columns >containing the annotation information associated >with the probes. Can I get differential >expression gene list according to GPR file >without sort so that I can copy and paste the >column gene info from GPR file into >toptable? I don???t want LIMMA to sort out the >genes for me. Many thanks. Best Regards, Wang >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu

Hi Jim, Thanks a lot for the kind help. I had solved the problem by using of sort=?none? option. Best Regards, Wang ----- Original Message ----- From: "James W. MacDonald" <jmacdon@med.umich.edu> To: "Jixin Wang" <jixinwang at="" neo.tamu.edu=""> Cc: bioconductor at stat.math.ethz.ch Sent: Tuesday, November 4, 2008 12:15:22 PM GMT -06:00 US/Canada Central Subject: Re: [BioC] LIMMA Sort problem If you don't want limma to sort things, then I believe what you want is write.fit(). Best, Jim Wang, Jixin wrote: > Dear All, > I have one question about the consistence between topTable output with GPR file. In my GPR file, I have several columns containing the annotation information associated with the probes. > Can I get differential expression gene list according to GPR file without sort so that I can copy and paste the column gene info from GPR file into toptable? I don?t want LIMMA to sort out the genes for me. > Many thanks. > Best Regards, > > Wang > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662