[BioC] create an new AnnotatedDataFrame

[Martin Morgan]

"GHAVI-HELM Yad" <yad.ghavi-helm at cea.fr> writes:

>
>
> exprsFile<-"D:/exprsData.txt"
> exprs<-read.table(exprsFile,header=TRUE,sep="",as.is=TRUE)
>
> pDataFile<-"D:/pData.txt"
> pData<-read.table(pDataFile,header=TRUE, sep="", as.is=TRUE)
>
> metaData<-"D:/mData.txt"
> mData<-read.table(metaData,header=TRUE,sep="",as.is=TRUE)
> metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData)
>
> At this step I have the following error: 
> Error in `row.names<-.data.frame`(`*tmp*`, value = c("A", "B")) : 
>         length of 'row.names' incorrect
>
> It seems strangle because "A" and "B" are the colnames of exprsData
> (or the rownames of pData).

AnnotatedDataFrame coordinates a data.frame with it's metadata. From
your naming convention, I'm guessing that what your command is doing
is trying to coordinate an expression matrix with its varMetadata. I
think what you want to do is

> phenoData = new("AnnotatedDataFrame", data=pData, varMetadata=mData)

You might then use this to create an ExpressionSet (for example)

> new("ExpressionSet", exprs=exprs, phenoData=phenoData)

The read.AnnotatedDataFrame page might provide some additional hints
on reading data from files; a warning is that read.AnnotatedDataFrame
will change (hopefully for the better) in the next release of
Bioconductor.

Hope that helps,

Martin

> I tried to do :
>
> metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData, row.names=1)
>
> or
>
> rown=rownames(exprs)
> metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData, row.names=rown)
>
>
> but I steel got the same error
>
> hope anyone could help me...
>
>
>> sessionInfo()
> R version 2.5.0 (2007-04-23) 
> i386-pc-mingw32 
>
> locale:
> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
>
> attached base packages:
>  [1] "tcltk"     "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     
>
> other attached packages:
>       YEAST     convert      marray   tkWidgets      DynDoc widgetTools  arrayMagic  genefilter    survival         vsn        affy      affyio       limma 
>    "1.16.0"    "1.10.0"    "1.14.0"    "1.14.0"    "1.14.0"    "1.12.0"    "1.14.0"    "1.14.1"      "2.31"     "2.2.0"    "1.14.2"     "1.4.1"    "2.10.5" 
>     Biobase 
>    "1.14.1" 
>  
>
>
> Yad.
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org