Dear Jenny and Gordon: Many thanks to you for your help. All you recommended work well for me. cheers! Jianping --On Thursday, June 01, 2006 9:52 AM -0500 Jenny Drnevich <drnevich at="" uiuc.edu=""> wrote: > Hi Jianping, > > I recently wrote a detailed response along these same lines for a client. > It's not as elegant as Gordon's solution, but it works for me and can be > modified for any combination you want: > > The coded.results object (output from 'decideTests') has the matrix of > -1, 0 , and 1s. If BvT and AvT are the 5th and 6th columns in the > coded.results object, you can do: > > BsameAup <- which(coded.results[,5] == 1 & coded.results[,6] == 1) > > This will give you a vector of row numbers you can use to subset most > other objects that have the genes in the same order: > > BsameAupgenes <- fit$genes[BsameAup,] #remember that between [], to the > left of the , refers to rows and to the right refers to columns > > You can actually combine these two steps if you want to get fancy: > > BsameAdowngenes <- fit$genes[coded.results[,5] == -1 & coded.results[,6] > == -1 , ] > > This subsetting uses TRUE/FALSE output (a conditional statement), such as > == (equal to), != (not equal to), >, <=, etc. > > BupAdown <- which(coded.results[,5] == 1,& coded.results[,6] != 1) > BchangedAnot <- which(coded.results[,5] != 0 & coded.results[,6] == 0) > > In case you want to use it, the "or" equivalent of "&" is "||" (two > straight characters, not the letter l or capital I; on my keyboard it is > on the same key as the backslash \). You can also put more than two > conditional statements together - just tack as many as you want using & > or ||. > > Cheers, > Jenny > > > At 09:23 AM 6/1/2006, jjin at email.unc.edu wrote: >> Hi Gordon, >> >> Thanks very much for your help! That is what I wanted to extract. But >> what if I wanted genes DE for "A" and "B" but "C"? Or just for "A", not >> "B" and "C"? >> >> best wishes! >> >> Jianping >> >> >> Quoting Gordon Smyth <smyth at="" wehi.edu.au="">: >> >> > Dear Jianping, >> > >> > I may be mis-interpreting your question (I'm not sure what you mean >> > by a "session"), but I think you just want the gene lists >> > corresponding to the counts in the Venn diagram. >> > >> > Suppose you have a fitted model 'fit' with columns "A", "B" and "C". >> > Then >> > >> > vennDiagram(fit) >> > >> > will give you a Venn diagram with 8 counts in it. You can do the >> > diagram in two steps >> > >> > results <- decideTests(fit) >> > vennDiagram(results) >> > >> > and this allows you to extract the gene lists. Suppose you want the >> > genes DE for both "A" and "B", you could use >> > >> > myGenes <- apply(results[,c("A","B")],1,all) >> > fit$genes[myGenes,] >> > >> > to see the gene list. >> > >> > Best wishes >> > Gordon >> > >> >> Date: Tue, 30 May 2006 13:22:08 -0400 >> >> From: Jianping Jin <jjin at="" email.unc.edu=""> >> >> Subject: [BioC] VennDiagram quesiont in limma >> >> To: BioConductor_list <bioconductor at="" stat.math.ethz.ch=""> >> >> Message-ID: <dbcd9d517c98493f3a37fa9d at="" unc-="" jpjin.pmbb.med.unc.edu=""> >> >> Content-Type: text/plain; charset=us-ascii; format=flowed >> >> >> >> Dear list: >> >> >> >> I am wondering if there is an easy way or a function by which one can >> >> extract (list) any session of genes, either in common or not in >> >> common >> with >> >> other sesseion(s), in vennDiagram of limma? I assumed that vennDiagram >> >> should be able to allow to do that. But I did not find anything like >> >> that after reading the on-line instructions. >> >> >> >> Many thanks if you could help me out! >> >> >> >> Jianping >> >> >> >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> >> x Jianping Jin Ph.D. x >> >> x Bioinformatics scientist x >> >> x Center for bioinformatics x >> >> x 3133 Bioinformatics Building x >> >> x CB# 7104 x >> >> x University of North Carolina x >> >> x Chapel Hill, NC 27599 x >> >> x Tel: (919)843-6105 x >> >> x Fax: (919)843-3103 x >> >> x E-mail: jjin at email.unc.edu x >> >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> > >> > >> >> _______________________________________________ >> 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 uiuc.edu xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin at email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx