[BioC] RE : create an new AnnotatedDataFrame

[GHAVI-HELM Yad]

Hi Martin,

>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.

In fact, that's exactely what I want to do.
Since I don't have any annotation package for the chips I'm using, 
I would like to add usefull informations (for exemple correspondance between oligs ID's and Genenames) in the mData.

My MetaData file looks like :

		gene	
A_75_P0000001	TEL01L	
A_75_P0000002	YAL067W-A	
A_75_P0000003	YAL067C	
A_75_P0000004	YAL067C	
A_75_P0000005	YAL067C	
A_75_P0000006	YAL067C	
A_75_P0000007	YAL067C	
A_75_P0000008	YAL067C	

with as many features as my assayData (exprs2)

I think it is possible to do this, because I read: 

"It is also possible to record information about features that are unique to the experiment 
(e.g.,flagging particularly relevant features). This is done by creating or modifying an Annotated
Data Frame like that for phenoData but with rownames of the AnnotatedDataFrame
matching rows of the assaydata."

in the Biobase "ExpressionSetIntroduction.pdf" manual.

Yad.


-------- Message d'origine--------
De: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Date: mer. 08/08/2007 18:54
À: GHAVI-HELM Yad
Cc: Bioconductor at stat.math.ethz.ch
Objet : Re: [BioC] create an new AnnotatedDataFrame
 
"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