Hi there, I am trying to use calculate p value and FDR for illumina microarry platform. I am really new to this field and found there are many package in bioconductor. Does anyone can give any recommendations? Thanks,Zhengyu [[alternative HTML version deleted]]

You might try looking at the limma package. If you are new to the field, it is a good idea to find a local collaborator to help you through the data. Sean On May 7, 2012 9:22 AM, "JiangZhengyu" <zhyjiang2006@hotmail.com> wrote: > > > > > Hi there, I am trying to use calculate p value and FDR for illumina > microarry platform. I am really new to this field and found there are many > package in bioconductor. Does anyone can give any recommendations? > Thanks,Zhengyu > [[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 > [[alternative HTML version deleted]]

I wish you could give more information such as what have you done with your data. Anyway, I tried Illumina before by using lumi and limma package. the latter give you p.value and adj.p.val. If I understand right, adj.p.val is similar to FDR. Good luck. Wenhuo Hu On May 7, 2012 9:22 AM, "JiangZhengyu" <zhyjiang2006@hotmail.com> wrote: > > > > > Hi there, I am trying to use calculate p value and FDR for illumina > microarry platform. I am really new to this field and found there are many > package in bioconductor. Does anyone can give any recommendations? > Thanks,Zhengyu > [[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 > [[alternative HTML version deleted]]

Hi Zhengyu, this does not need to be Bioc specific, the R internal function will do, ? p.adjust you may also have a look at package qvalue, http://www.bioconductor.org/packages/release/bioc/html/qvalue.html HTH Dan On Mon, 2012-05-07 at 21:21 +0800, JiangZhengyu wrote: > > > > Hi there, I am trying to use calculate p value and FDR for illumina microarry platform. I am really new to this field and found there are many package in bioconductor. Does anyone can give any recommendations? Thanks,Zhengyu > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor