Hi Martha, What I've done to compare the results of different analyses is to create a new "TestResults" object combining the output of several different decideTests: > results1 <- decideTests(fit1) > results2 <- decideTests(fit2) > results3 <- decideTests(fit3) > results.all <- new("TestResults",cbind(results1, results2, results3)) # results 1-3 must have rows all in the same order vennCounts() and vennDiagram() will now work with results.all, but you'll have to pick up which 3 columns if you have more than that. vennSelect() probably won't work (I never use it so I haven't tried), so if you want to create gene lists rather than number comparisons, you'll have to do it manually, e.g.: > genelist <- fit1$genes[results.all[,1] ==1 & results.all[,3] ==1, ] Cheers, Jenny At 04:17 PM 11/19/2009, Martha Behnke wrote: >Hello all, > >I am working with data with a very large number of differentially expressed >genes (liver cancer samples), and wish to demonstrate for my advisor and >committee the effect of choosing different pre-processing methods. To do >this, I have normalized the data in several different ways and genereated >DEG lists with limma and decideTests. Now I would like to examine the >difference in which probesets are called by the various methods. > >I've read everything I can find about the venn tools in limma and >vennSelect, but they only seem to compare the output of different contrasts >within a single dataset. Can someone suggest how to compare the output of >the same contrast in a dataset processed 2 ways? I could output to >Microsoft Access, but surely there is a better way!! > >Thanks so much, >Mikki Behnke >Integrative Life Sciences >Virginia Commonwealth University > > [[alternative HTML version deleted]] > >_______________________________________________ >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