[BioC] error coercing an exprSet to ExpressionSet

[Kimpel, Mark William]

Seth,

You are correct. justRMA is not giving rownames to the se.exprs slot.
Below is the nice output I got after following your advice.

At some point in the future will justRMA and other background
correction/normalization routines in Affy be outputting ExpressionSet
rather than the deprecated exprSet?

> rownames(se.exprs(eset)
+ )
NULL
> 
> rownames(se.exprs(eset))<-rownames(exprs(eset))
> 
> as(eset,"ExpressionSet")
ExpressionSet (storageMode: lockedEnvironment)
assayData: 8799 features, 59 samples 
  element names: exprs, se.exprs 
phenoData
  sampleNames: WS02R111.CEL, WS02R112.CEL, ..., WS02R526.CEL (59 total)
  varLabels and varMetadata:
    sampleNames: read from file
    Strain: read from file
    Region: read from file
    Animal: read from file
featureData
  featureNames: A01157cds_s_at, A03913cds_s_at, ..., Z96106_at (8799
total)
  varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] "rgu34a"

Mark W. Kimpel MD 

 

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-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon
Sent: Thursday, November 16, 2006 10:41 PM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] error coercing an exprSet to ExpressionSet

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:

> Seth,
>
> Didn't work, here's what I got for output:
>
> as(eset,"ExpressionSet")
> Error in validObject(.Object) : invalid class "ExpressionSet" object: 
> featureNames differ between AssayData members

Here's my guess of what's going on.  Does your exprSet, eset, have
data in both the exprs and se.exprs slot?  I suspect that the answer
is yes and that the rownames of these two matrices do not match (this
is what the error is telling us).

So I would compare rownames(se.exprs(eset)) with rownames(exprs(eset))
and make them match.  Then try the convert again.

+ seth

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