To whom it may concern. Hello, I am new in microarray data analysis. recently I want to use Limma to find different expressed genes between grade I and grade III, which you could see from the annotation file. but when I use the R code below to do this, I only got two different expressed genes, could anybody tell me why? Is there anything wrong with my code? thank you in advance! and the data is available on line.http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2990 ? Best regards, yongzi Best wishes to you! ====================================================== Yong-Zi Chen, Ph.D. ? Tianjin Cancer Institute Tianjin Medical University Cancer Institute and Hospital Huan-Hu-Xi Road, Ti-Yuan-Bei, He-Xi District Tianjin300060, P.R. China Phone&Fax:?? 0086-022-23340123 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: GSE2990_suppl_new.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20130617="" bbe7497c="" attachment.txt="">

Hi Yongzi, The file you attached doesn't seems to be a valid. Please use raw files from the GEO page. Also, you might want to put your code in mail. Atul On 06/16/2013 09:31 PM, yongzi chen wrote: > To whom it may concern. > > Hello, I am new in microarray data analysis. recently I want to use Limma to find different expressed genes between grade I and grade > III, which you could see from the annotation file. but when I use the R > code below to do this, I only got two different expressed genes, could > anybody tell me why? Is there anything wrong with my code? thank you in > advance! and the data is available on line.http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2990 > > > Best regards, > > yongzi > > > > Best wishes to you! > > > ====================================================== > Yong-Zi Chen, Ph.D. > > Tianjin Cancer Institute > Tianjin Medical University Cancer Institute and Hospital > Huan-Hu-Xi Road, Ti-Yuan-Bei, He-Xi District > Tianjin300060, P.R. China > Phone&Fax: 0086-022-23340123 > > > _______________________________________________ > 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 [[alternative HTML version deleted]]