[BioC] Analysis of Affymetrix Mouse Gene 2.0 ST arrays

[Naxerova, Kamila]

Dear all,

I am afraid I have to ask for help with the Mouse Gene 2.0 ST annotation package one more time. It looked like I created it successfully, but when I try to use it to read in cel files with the oligo package, I get a cryptic error message. Any suggestions would be much appreciated!

> abatch <- read.celfiles(list.celfiles(),pkgname="mogene20sttranscriptcluster.db")
Platform design info loaded.
Reading in : xxx.CEL
Reading in : xxx.CEL
Reading in : xxx.CEL
[... more cel files listed]

Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘kind’ for signature ‘"ChipDb"’

Thanks
Kamila

On Mar 6, 2013, at 6:16 PM, "Naxerova, Kamila" <naxerova at fas.harvard.edu> wrote:

> Dear Christian and Jim,
> 
> many thanks to both of you for your explanations. 
> 
> Your hard work paid off, and I have finally understood everything and managed to build my annotation package!!!! I wrote a little script similar to what Jim was suggesting, namely picking the first RefSeq-like thing I came across. Jim called it "naive" -- but I think there is no downside to this approach, right? I have looked at various examples in the Affy file for a long time, and simply picking the first Refseq ID seems to be kosher.
> 
> data <-read.csv("MoGene-transcript-noheader.csv",header=T,stringsAsFactors=F,sep=",")
> sdata <- data[,c(1,9)]
> 
> returnRef=function(x){
> 	refst <- strsplit(x,split="///")[[1]][grep("RefSeq",strsplit(x,split="///")[[1]])[1]]
> 	refid <- gsub(" ","",strsplit(refst,split="//")[[1]][1])
> 	return(refid)
> }
> 
> sdata$refseqids <- sapply(sdata[,2],returnRef)
> fdata <- sdata[,-2]
> write.table(fdata,"AnnotBuild.txt", sep="\t",quote=F,row.names=F,col.names=F)
> 
> library(AnnotationForge)
> library(mouse.db0)
> library(org.Mm.eg.db)
> makeDBPackage("MOUSECHIP_DB",
> affy=F,
> prefix="mogene20sttranscriptcluster",
> fileName="AnnotBuild.txt",
> outputDir = ".",
> version="2.11.1",
> baseMapType="refseq",
> manufacturer = "Affymetrix",
> chipName = "Mouse Gene 2.0 ST Array",
> manufacturerUrl = "http://www.affymetrix.com",
> author = "Kamila Naxerova",
> maintainer = "Kamila Naxerova <naxerova at fas.harvard.edu>")
> 
>> install.packages("mogene20sttranscriptcluster.db",repos=NULL, type="source")
> * installing *source* package ‘mogene20sttranscriptcluster.db’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> *** arch - i386
> *** arch - x86_64
> 
> * DONE (mogene20sttranscriptcluster.db)
> 
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