[BioC] problem to obtain exprset using GEOquery

[Stephen Henderson]

You can't. The information in the GSE object and the exprSet object
contain probeset summary data i.e the summary of 11 probes into 1
probeset value. rma uses all probes to create a probeset summary too.
You need the CEL files and only some GEO entries supply these-- although
occasionally the SOFT files contain rma data already.


Stephen Henderson
Wolfson Inst. for Biomedical Research
Cruciform Bldg., Gower Street
University College London
United Kingdom, WC1E 6BT
+44 (0)207 679 6827


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Alberto
Goldoni
Sent: 13 July 2006 11:19
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] problem to obtain exprset using GEOquery

I have converted a GSE object to an exprSet object "eset2" just in the
vignette but I wanna analyze microarray dataset again for example with:
 
  
 
 usually starting from CEL files i should edit:
 
  
 
 data<-ReadAffy(widget=T)
 
  
 
 pData(data)
 
  
 
 and then:
 
  
 
 data.rma<-rma(data) # for example!
 
  
 
 BUT STARTING FROM THE exprSet object "eset2" HOW CAN PROCEDE IN ORDER 
 TO
 reanalyze microarray
 
if i write:
 
            eset2.rma<-rma(eset2)
Errore in probeNames(object, subset) : no direct or inherited method for
function 'probeNames' for this call
 
 
where 
> eset2
Expression Set (exprSet) with 
      22283 genes
      76 samples
             phenoData object with 1 variables and 76 cases
       varLabels
            : samples
 
how can I do to create an affybatch object in order to use rma function
on my dataset?
 
ps: to obtain eset2 I have followed the instruction on the GEOquery
vignette:
 
> probesets <- Table(GPLList(gse)[[1]])$ID
> data.matrix <- log2(do.call("cbind", lapply(GSMList(gse), function(x)
{
+ tab <- Table(x)
+ mymatch <- match(probesets, tab$ID_REF)
+ return(tab$VALUE[mymatch])
+ })))
> rownames(data.matrix) <- probesets
> colnames(data.matrix) <- names(GSMList(gse))
> pdata <- data.frame(samples = names(GSMList(gse)))
> rownames(pdata) <- names(GSMList(gse))
> pheno <- new("phenoData", pData = pdata, varLabels =
as.list("samples"))
> eset2 <- new("exprSet", exprs = data.matrix, phenoData = pheno)
> eset2
 
 
 
Dr Alberto Goldoni
Medical Genetics Unit
S. Orsola-Malpighi Hospital
Via Massarenti n.9, Pad 11
40100 Bologna, Italy
Mobile Phone: 338-4145970
Fax: 051-636-4004
 <mailto:alberto.goldoni at eurogene.org> alberto.goldoni at eurogene.org
 <http://www.eurogene.org> www.eurogene.org
 <http://www.lagem.it> www.lagem.it
 

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