Search
Question: Fwd: error with Two class paired in samr function
0
gravatar for John Antonydas Gaspar
9.3 years ago by
John Antonydas Gaspar130 wrote:
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 ----- ----- 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="" d5fa5f9f="" attachment.txt="">
ADD COMMENTlink written 9.3 years ago by John Antonydas Gaspar130
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 122 users visited in the last hour