[BioC] Manual annotation of ExpressionSet object created from scratch

Michael Muratet mmuratet at hudsonalpha.org
Tue Oct 14 00:00:21 CEST 2008

On Oct 13, 2008, at 4:48 PM, Sean Davis wrote:

> On Mon, Oct 13, 2008 at 5:34 PM, Michael Muratet
> <mmuratet at hudsonalpha.org> wrote:
>> Greetings
>> I have an ExpressionSet object that I created from scratch with  
>> expression
>> data for features identified with Ensembl transcript IDs. The  
>> ExpressionSet
>> constructor wants a character string for annotation data. Is there  
>> another
>> way to populate the slot? From an AnnotatedDataFrame? Should I  
>> write a
>> function that pulls in the data with biomaRt?
> Hi, Mike.  Perhaps you can show us what you mean.  If you are talking
> about the annotation data slot, that is meant to be the string name of
> the annotation data package associated with the array.  I guess that
> you do not have an annotation data package for the array, so you can
> leave out that slot when creating the ExpressionSet.  If you have
> problems, it is best to post the code and, of course, your
> sessionInfo().


Here's what I'm trying to do....

> library("Biobase")
> exprMatrix <- as.matrix(read.table("exprset.txt", header=TRUE,  
> sep="\t", row.names=1, as.is=TRUE))
> pData <- read.table("phenoData.txt", row.names=1, header=TRUE,  
> sep="\t")
> phenoData <- new("AnnotatedDataFrame", data=pData)
> rnaseq_exprs <- new("ExpressionSet", exprs=exprMatrix,  
> phenoData=phenoData)
> save(rnaseq_exprs, file="rnaseq_data.Robj")

The data consists of RNAseq reads that I have mapped to Ensembl  
transcripts and normalized appropriately, e.g.,

         SL265   SL264   SL266   SL310   SL312   SL313
ENST00000369829 0       0       0       0.00288159443768686      
0.000696405393229021    0.000473063478950364
ENST00000393415 0       0       0       0.000428628056614047     
0.000621528594887718    0.00047497519763826

So far this looks like a fairly useful way of looking at the data.

I'd like to be able to use all the functionality I see in the docs for  
annotation of ExpressionSets. The ExpressionSet vignette talks about  
using an AnnotatedData frame but it doesn't really say where it goes.  
I haven't seen an annotation data package for Ensembl although I see  
how you might be able to create one with biomaRt. I'm looking for some  
expert advice so I don't go down any blind alleys.



> Sean
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