[BioC] Bioconductor Digest, Vol 117, Issue 6

[Dick Beyer]

Hi Sainitin,

I'd guess your problem is your "s"i matrix.  I say that because of your line of code:
si.gnames<-si[,1]

If you are send "si" to RPadvance, then RPadvance doesn't know what to do with the first column, as it thinks that should be numerical.

Cheers,
Dick 
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Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
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>
> Message: 1
> Date: Sun, 4 Nov 2012 13:01:49 +0100
> From: sai nitin <sainitin7 at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] Rank Product question.
> Message-ID:
> 	<CAGJtc4OCJd2MTbUgx8x8NNtPvhbQcSFstYfLdmCeqN8jVg1yXQ at mail.gmail.com>
> Content-Type: text/plain
>
> Hi all,
>
> I have expression data from 3 different laboratories i wanted perform meta
> analysis using rank product package i wrote following code having 21
> samples
>
> library(RankProd)
>
> #loading normalized data
>
> si<-read.table("affy_all.txt",sep="\t",header=TRUE,as.is=T)
>
> #reading affy ids
>
> si.gnames<-si[,1]
>
> #Creating class variables
>
> si1<-7
>
> si2<-14
>
> si.cl<-rep(c(0,1),c(si1,si2))
>
> 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1
>
> #Creating origin variable
>
> si.origin<-c(rep(1,6),rep(2,3),rep(3,12))
>
> 1 1 1 1 1 1 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3
>
> #Identifying regulated genes
>
> RP.adv.out<-RPadvance(si,si.cl,si.origin,num.perm=100,na.rm=FALSE,gene.names
> =si.gnames,rand=123)
>
> *But it gives error :( as follows*
>
> *Error in RPadvanceV1(data, cl, origin, num.perm, logged, na.rm,
> gene.names,  :
> *
>
> *  Number of classes and/or origins should match the columns in the data*
>
>
> I checked my data it is correct ...couldnt figure out problem
>
>
> Can any any body help
>
>
> Thanks in Advance,
>
> Sainitin
>
>
> -- 
>
> Sainitin D
> PhD student
> Biotechnology Center
> Technische Universit?t Dresden
> Tatzberg 47/49
> 01307 Dresden, Germany
>