[BioC] error coercing an exprSet to ExpressionSet

[Kimpel, Mark William]

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

Enter a frame number, or 0 to exit   

 1: as(eset, "ExpressionSet")
 2: asMethod(object)
 3: new("ExpressionSet", phenoData = as(phenoData(from),
"AnnotatedDataFrame"), experimentData = desc, annotation =
annotation(from), exprs = exprs, se.exp
 4: initialize(value, ...)
 5: initialize(value, ...)
 6: .local(.Object, ...)
 7: callNextMethod(.Object, assayData = assayData, phenoData =
phenoData, featureData = featureData, experimentData = experimentData,
annotation = annotati
 8: eval(call, callEnv)
 9: eval(expr, envir, enclos)
10: .nextMethod(.Object, assayData = assayData, phenoData = phenoData,
featureData = featureData, experimentData = experimentData, annotation =
annotation)
11: .local(.Object, ...)
12: callNextMethod(.Object, assayData = assayData, phenoData =
phenoData, featureData = featureData, experimentData = experimentData,
annotation = annotati
13: eval(call, callEnv)
14: eval(expr, envir, enclos)
15: .nextMethod(.Object, assayData = assayData, phenoData = phenoData,
featureData = featureData, experimentData = experimentData, annotation =
annotation)
16: .local(.Object, ...)
17: callNextMethod(.Object, ...)
18: eval(call, callEnv)
19: eval(expr, envir, enclos)
20: .nextMethod(.Object, ...)
21: validObject(.Object)

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 8:18 PM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] error coercing an exprSet to ExpressionSet

Hi Mark,

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
> I have encountered an error when attempting to coerce an exprSet to an
> ExpressionSet. Below is my code, output, and sessionInfo(). What is
> the problem? Thanks, Mark
>
>>isCurrent(eset, "exprSet")
>                R Biobase annotatedDataset exprSet TRUE TRUE TRUE TRUE
>>  as(exprSet=eset,"ExpressionSet")
> Error in as(exprSet = eset, "ExpressionSet") : unused argument(s)
> (exprSet = <S4 object of class "exprSet">)

Can you try again without naming the argument?  Like this:

   ans <- as(eset, "ExpressionSet")

The error message is telling you that 'exprSet' is not one of the
formal arguments to the as function.  You can see those arguments
using the args() function:


    > args(as)
    function (object, Class, strict = TRUE, ext =
possibleExtends(thisClass, 
        Class)) 

So if you wanted, you could call as(object=eset, Class="ExpressionSet").

Hope that gets you going again.


+ seth

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