Hello you, i have a problem using Rankproduct: I read the papers of Rainer Breitling and the Rank Product Vignetes but still have questions about this method 1. I tried to calculate the Rank product in Excell (as explain in the paper of Rainer Breitling) using a small data set, i didn't get the same results as calculating it with R-Programm. Can somebody help me? 2. How can i understand the results obtaining from Rankproduct for example: class1 = c(rep(0,40)) class2 =c( rep(1, 24)) cl<-c(rep(0,40), rep(1,24)) Table 1 class1<class2: is="" that="" the="" up-regulated="" genes="" in="" classs1="" compare="" to="" class="" 2?="" table="" 2:="" class1="">class2: Is that the down-regulated genes in class1 compare to class2? 3. How does R-Programm calculates the RP/Rsum? Thanks for your help _________________________________________________________________ Haben Spinnen Ohren? Finden Sie es heraus ? mit dem MSN Suche Superquiz via http://www.msn-superquiz.de Jetzt mitmachen und gewinnen!

Hi Nadine, > 1. I tried to calculate the Rank product in Excell (as explain in the > paper > of Rainer Breitling) using a small data set, i didn't get the same > results > as calculating it with R-Programm. > Can somebody help me? The RankProd package under bioconductor is programmed according to the original paper by Rainer, which means the results should be similar if you program it in excel according to the paper too. You might observe small difference which is due to different random number generator used in Excel and in R. > 2. How can i understand the results obtaining from Rankproduct > for example: > class1 = c(rep(0,40)) > class2 =c( rep(1, 24)) > > cl<-c(rep(0,40), rep(1,24)) > Table 1 class1<class2: is="" that="" the="" up-regulated="" genes="" in="" classs1="" compare=""> to > class 2? > Table 2: class1>class2: Is that the down-regulated genes in class1 compare > to class2? The two tables are explained in package vignette, I will double check to make sure that it is up to date. Since it is class1<class2, table="" 1="" lists="" genes="" that="" are="" up-regulated="" in="" class2="" compared="" with="" class="" 1.="" and="" table="" 2(class1=""> class2) lists genes that are down-regulated in class 2 compared with class 1. > > 3. How does R-Programm calculates the RP/Rsum? If you call RP or RPadvance, the output is RP;if you call RSadvance, it is Rsum. For RP, it is programmed according to the original paper. For Rsum, instead of getting produce of rank, it compute the average rank. Hopefully this helps. fangxin > Thanks for your help > > _________________________________________________________________ > Haben Spinnen Ohren? Finden Sie es heraus ? mit dem MSN Suche Superquiz > via > http://www.msn-superquiz.de Jetzt mitmachen und gewinnen! > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -------------------- Fangxin Hong Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong at salk.edu (Phone): 858-453-4100 ext 1105