Hi Qicheng. An FDR can be calculated from the null distribution, but the software doesn't do it. For example, see:
http://bioinformatics.oxfordjournals.org/cgi/content/full/21/23/4280 The code below may give a useful plot, basically the MUF scores for the dataset, with boxplots of the null distributions overlaid: matplot( jitter(fg$nProbe), abs(fg$mufScores), pch=19, cex=.2, xlim=c(7,80), xlab="Number of Probes", ylab="MUF scores", xaxt="n") boxplot( fg$nullDistributions, at=1:length(fg$nullDistributions), add=TRUE, boxwex=.4, outline=FALSE, names=NULL, las=2, yaxt="n", col="orange" ) Cheers, Mark On 2010-08-12, at 12:39 AM, Qicheng Ma wrote: > Hi, > > I looked at the results, fg, > > > names(fg) > [1] "mufScores" "firmaGeneScores" "nProbe" > [4] "nullDistributions" "nProbeNull" "plmObject" > [7] "cls" > > There is no Pvalue (or Qvalue), but the paper says: > > "To alleviate this, we repeatedly sample J probes from > the empirical distribution of all standardized residuals > and calculated the MUF score, giving a null distribution of > MUF scores for J probes. A false discovery rate can be calculated > for the discoveries above a given quantile of the > null distributions." > > How can I get the Qvalue from false discovery rate ? > > Thanks, > > Qicheng > ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
