________________________________________ From: Fatemehsadat Seyednasrollah Sent: Wednesday, July 11, 2012 1:01 PM To: Simon Anders Subject: RE: [BioC] Reproducibility in DESeq Hi, Thanks a lot, I would be so grateful if you suggest a parameter to choose for obtaining this rank for reproducibility? With Best Regards, Narges ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] on behalf of Simon Anders [anders@embl.de] Sent: Wednesday, July 11, 2012 12:55 PM To: bioconductor at r-project.org Subject: Re: [BioC] Reproducibility in DESeq Hi, On 07/11/2012 11:00 AM, Fatemehsadat Seyednasrollah wrote: > I have several subsets of a datasets from one RNA seq experiment and > I need to compare the reproducibility of these different subsets with > DESeq. I have both FDR and P values for each gene in my subsets and I > need to transform P value or FDR to RANK coordination. Then I can > plot the reproducibility(y axis) according to this rank(x axis) which > has obtained from p value or FDR for each differentially expressed > gene. Any idea for transforming one of these parameters to obtain a > rank?(I should transform p value or fdr to this rank and use it as x > axis of my plot). To convert a list of values to ranks in R, simply use the 'rank' function. However, I am rather sceptical that comapring ranks of p values is a suitable method to assess reproducibility of an experiment. Simon _______________________________________________ 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