Hi Claire, > Hi, > I have been investigating using the RP package for data anaylsis (the vignette was really helpful, thanks!) and I have a couple of points I was unsure of. First of all I have 2 probesets (212280_x_at and > 1557984_s_at) that appear once in the list of upregulated probesets and once in the list of down-regulated probesets, why does this happen? I need a little more information here. Did you mean that you run Rank Product using different random number generator, these two genes appear to be upregulated once and down-regulated once? Since rank product searches for up-regulated genes and down-regulated genes separately, this would be possible when the behavior of this gene is really inconsistent, meaning having really large fold change from some replicates and really small food-change under some other replicates. I would suggest that you check the average fold-change output from topGene, and the Orirank output from RP ( which is accessed by rp.out$Orirank[[1]]: fro the up-regulation search, rp.out$Orirank[[2]] for the down-regulation search) to double check the identified genes. > Also > for 1 probeset (1557984_s_at), fold changes are greater than 1 in the downregulated list but less than 1 in the upregulated list. This is strange since the fold changes are computed once, it should be the same value no matter which list this probeset appears? > Any ideas why this is happening? I have included the relevant sections from $Table1 and $Table2 in the attached file If you can send me the data set, rma.eset at exprs, I might be able to check it . Thanks. Fangxin > library(RankProd) > data.classes <- c(0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1) > rp.out <- > RP(rma.eset at exprs,data.classes,gene.names=rownames(rma.eset at exprs),rand123) output <- > rbind(topGene(rp.out,cutoff=0.05)$Table1,topGene(rp.out,cutoff=0.05) $Tab le2) > annot <- > read.csv("/users/cwilson/ying/annotAug05.txt",header=T,sep="\t") tmp <- annot[,2:3] > rownames(tmp) <- annot[,1] > annot <- tmp > output <- cbind(annot[output[,1],],output) > write.table(x=output,file="rp_out.xls",quote=F,sep="\t") > -- > Claire Wilson > Bioinformatics Group > Paterson Institute for Cancer Research > Christie Hospital NHS Trust > Wilmslow Road > Manchester > M20 4BX > tel: +44 (0)161 446 8218 > url: http://bioinf.picr.man.ac.uk/bioinf/cwilson.jsp > <http: bioinf.picr.man.ac.uk="" bioinf="" cwilson.jsp=""> > -------------------------------------------------------- > This email is confidential and intended solely for the use...{{dropped}}