mva.pairs

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mva.pairs

Vijay A Raghavan
Hello,
 
 I am using the following code to plot an MVA plot.
 
 library(affy)
 library(Biobase)
 library(limma)
 library(gcrma)
 
     pd<-read.phenoData("Clk.targets.2.txt",header=TRUE,
     row.names=1,as.is=TRUE,sep="\t")
     Data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd)
     Print(Data)
     
     eset <- gcrma(Data)
     write.exprs(eset, file="clk.6-23-05.txt")
       
         
     bitmap("clk-1.mva.jpg",width=15, height=12)
     mva.pairs(exprs(eset)[,c(19,20,21,22,23,24)],log.it=FALSE)
     dev.off()
 
 but I am getting an subscript out of bound error.
 
 Any Idea ?
 
 Thanks,
 
 Vijay
 
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Re: mva.pairs

James W. MacDonald
Hi Vijay,

Vijay A Raghavan wrote:

> Hello,
>  
>  I am using the following code to plot an MVA plot.
>  
>  library(affy)
>  library(Biobase)
>  library(limma)
>  library(gcrma)
>  
>      pd<-read.phenoData("Clk.targets.2.txt",header=TRUE,
>      row.names=1,as.is=TRUE,sep="\t")
>      Data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd)
>      Print(Data)
>      
>      eset <- gcrma(Data)
>      write.exprs(eset, file="clk.6-23-05.txt")
>        
>          
>      bitmap("clk-1.mva.jpg",width=15, height=12)
>      mva.pairs(exprs(eset)[,c(19,20,21,22,23,24)],log.it=FALSE)
>      dev.off()
>  
>  but I am getting an subscript out of bound error.
>  
>  Any Idea ?

The only reason I know for getting a subscript out of bound error is
actually trying to subset an object using dimensions larger than the
object itself. In other words, do you really have 24 columns (e.g., 24
chips) in your exprSet?

>  
>  Thanks,
>  
>  Vijay
>  
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html


--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

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