[BioC] error with Two class paired in samr function

[John Antonydas Gaspar]

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





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