[BioC] VSN error : 'ny' does not seem to be resulting from vsn

[Wolfgang Huber]

Hi Saurin,

I answer your questions in reverse order: the error message in vsnPlotPar
results from using the option 'describe.preprocessing=FALSE' in the call
to vsn. If you use that option, the fitted parameters are not stored in
the resulting exprSet, hence there is nothing to plot for vsnPlotPar.

Second, what happens if you do esetSub2[,4:6]?
And what happens if you call vsn with describe.preprocessing=TRUE (i.e.
the default)?

If the problem persists, please make the exprSet available so I can have a
look.

Bw
 Wolfgang

<quote who="Saurin Jani">
> Hi,
>
> I am using R-2.0 with develOK=TRUE. Here, esetSub2 is
> my differentially expressed gene expression set.
>
>>esetSub2X <- getIntensityMatrix(esetSub2);
>
>>esetSub2Norm <- vsn(esetSub2,describe.preprocessing =
>
>  FALSE);
> vsn: 762 x 6 matrix (1 stratum). Please wait for 10
> dots: ..........
>
>> esetSub2Train <- esetSub2Norm[,4:6];
> Error in validObject(.Object) : Invalid "phenoData"
> object: FALSE
>
>> traceback();
> 7: stop(paste("Invalid \"", Class, "\" object: ",
> errors, sep = ""))
> 6: validObject(.Object)
> 5: initialize(value, ...)
> 4: initialize(value, ...)
> 3: new("phenoData", pData = pD, varLabels = vL)
> 2: phenoData(x)[j, , ..., drop = FALSE]
> 1: esetSub2Norm[, 4:6]
>
>> vsnPlotPar(esetSub2Norm, "factors")
> Error in vsnPlotPar(esetSub2Norm, "factors") :
>         'ny' does not seem to be resulting from vsn.
>
>> vsnPlotPar(esetSub2Norm, "offsets")
> Error in vsnPlotPar(esetSub2Norm, "offsets") :
>         'ny' does not seem to be resulting from vsn.
>
>> traceback();
> 2: stop("'ny' does not seem to be resulting from
> vsn.")
> 1: vsnPlotPar(esetSub2Norm, "offsets")
>
>
> is something wrong in my expression set?
>
> thank you,
> Saurin
>
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>


-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Http:  www.dkfz.de/abt0840/whuber
-------------------------------------

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Http:  www.dkfz.de/abt0840/whuber