Dear friends, Kindly help me out to trouble shoot. I am interested to find out Differentially Expressed genes betwenn control group(triplicates) and treated group (triplicates). I am trying with the followin coding using samr but ended up with error. ----- library(samr) Data1<-read.table("normalized.txt",sep="\t",header=TRUE,dec = ".",as.is =TRUE,na.strings = "NA", colClasses = NA,check.names = FALSE,strip.white = FALSE, blank.lines.skip = TRUE, allowEscapes = FALSE, flush = FALSE,encoding = "unknown") dim(Data1) [1] 27046 7 > de=Data1[,2:7] > de.gnames=Data1[,1] > de.cl=c(-1,-1,-1,1,1,1) > d=list(x=de,y=de.cl,geneid=as.character(de.gnames),genenames=de.gnames ,logged2=FALSE) > samr.obj<-samr(d,resp.type="Two class paired", nperms=100, return.x=FALSE, knn.neighbors = 50, random.seed=NULL) Error in o1[j] <- (1:ncol(x))[y == -o[j]] : replacement has length zero In addition: Warning message: In o1[j] <- (1:ncol(x))[y == -o[j]] : number of items to replace is not a multiple of replacement length ---------------------------------------- Herewith I have attached the normalixed data set also. I would greately appreciate the help With kind regards, antony -- John Antonydas Gaspar, Phd Student AG: Prof.A.Sachinidis Institute of Neurophysiology University of Cologne Robert-Koch-Str. 39 50931 Cologne/Germany Tel: 004922125918042 Handy: 004917683142627 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: normalized.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20090810="" 6d40acd3="" attachment-0001.txt="">

Dear friends, Kindly help me out to trouble shoot. I am interested to find out Differentially Expressed genes betwenn control group(triplicates) and treated group (triplicates). I am trying with the followin coding using samr but ended up with error. ----- library(samr) Data1<-read.table("normalized.txt",sep="\t",header=TRUE,dec = ".",as.is =TRUE,na.strings = "NA", colClasses = NA,check.names = FALSE,strip.white = FALSE, blank.lines.skip = TRUE, allowEscapes = FALSE, flush = FALSE,encoding = "unknown") dim(Data1) [1] 27046 7 > de=Data1[,2:7] > de.gnames=Data1[,1] > de.cl=c(-1,-1,-1,1,1,1) > d=list(x=de,y=de.cl,geneid=as.character(de.gnames),genenames=de.gnames ,logged2=FALSE) > samr.obj<-samr(d,resp.type="Two class paired", nperms=100, return.x=FALSE, knn.neighbors = 50, random.seed=NULL) Error in o1[j] <- (1:ncol(x))[y == -o[j]] : replacement has length zero In addition: Warning message: In o1[j] <- (1:ncol(x))[y == -o[j]] : number of items to replace is not a multiple of replacement length ---------------------------------------- Herewith I have attached the normalixed data set also. I would greately appreciate the help With kind regards, antony -- John Antonydas Gaspar, Phd Student AG: Prof.A.Sachinidis Institute of Neurophysiology University of Cologne Robert-Koch-Str. 39 50931 Cologne/Germany Tel: 004922125918042 Handy: 004917683142627 ----- End forwarded message ----- -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: normalized.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20090810="" 4400a38a="" attachment-0002.txt=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: normalized.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20090810="" 4400a38a="" attachment-0003.txt="">