Hi Sainitin, I'd guess your problem is your "s"i matrix. I say that because of your line of code: si.gnames<-si[,1] If you are send "si" to RPadvance, then RPadvance doesn't know what to do with the first column, as it thinks that should be numerical. Cheers, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/members_fc_IEHSFC.html http://staff.washington.edu/dbeyer ********************************************************************** ********* > > Message: 1 > Date: Sun, 4 Nov 2012 13:01:49 +0100 > From: sai nitin <sainitin7 at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] Rank Product question. > Message-ID: > <cagjtc4ocjd2mtbugx8x8nntpvhbqcsfstyfldmceqn8jvg1yxq at="" mail.gmail.com=""> > Content-Type: text/plain > > Hi all, > > I have expression data from 3 different laboratories i wanted perform meta > analysis using rank product package i wrote following code having 21 > samples > > library(RankProd) > > #loading normalized data > > si<-read.table("affy_all.txt",sep="\t",header=TRUE,as.is=T) > > #reading affy ids > > si.gnames<-si[,1] > > #Creating class variables > > si1<-7 > > si2<-14 > > si.cl<-rep(c(0,1),c(si1,si2)) > > 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > > #Creating origin variable > > si.origin<-c(rep(1,6),rep(2,3),rep(3,12)) > > 1 1 1 1 1 1 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 > > #Identifying regulated genes > > RP.adv.out<-RPadvance(si,si.cl,si.origin,num.perm=100,na.rm=FALSE,ge ne.names > =si.gnames,rand=123) > > *But it gives error :( as follows* > > *Error in RPadvanceV1(data, cl, origin, num.perm, logged, na.rm, > gene.names, : > * > > * Number of classes and/or origins should match the columns in the data* > > > I checked my data it is correct ...couldnt figure out problem > > > Can any any body help > > > Thanks in Advance, > > Sainitin > > > -- > > Sainitin D > PhD student > Biotechnology Center > Technische Universit?t Dresden > Tatzberg 47/49 > 01307 Dresden, Germany >