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

[Wolfgang Huber]

Hi Saurin,

it seems that the exprSet that in your case comes out of vsn is somehow
invalid, but I am not sure why. To debug this, can you please send me the
.rda file with esetSub2? (Offline, not to the list).

Best wishes
 Wolfgang



<quote who="Saurin Jani">



> Hi Dr. Huber,
>
> I have done as kept vsn with default TRUE value but I
> come up with same error for esetSubNorm[,4:6]
>
> I have 6 CEL files and I am reading through
> Readaffy().I am comparing Knock Out (KO) and Wild
> Type(WT) samples from Mouse embryo Fibroblast Affy
> data.
>
> I have below described expression set, please let me
> know if you need more values or informatoin for
> expression set.
>
>
>> library(vsn);
>> library(stam);
>
>> esetSub2Norm <- vsn(esetSub2);
> vsn: 762 x 6 matrix (1 stratum). Please wait for 10
> dots: ..........
>> vsnPlotPar(esetSub2Norm, "offsets")
>
> Here, vsnPlotPar works nice.
>
> But
>
>> esetSub2Train <- esetSub2Norm[,4:6];
> Error in validObject(.Object) : Invalid "phenoData"
> object: FALSE
>
>> phenoData(esetSub2);
>          phenoData object with 3 variables and 6 cases
>          varLabels
>                 sample: arbitrary numbering
>
>
>> pData(esetSub2);
>           sample scanner1 scanner2
> Fib1C-KO1      1        0       KO
> Fib1C-KO2      2        0       KO
> Fib1C-KO3      3        0       KO
> Fib1C-WT1      4        1       WT
> Fib1C-WT2      5        1       WT
> Fib1C-WT3      6        1       WT
>
>
>> exprs(esetSub2)
>
> Fib1C-KO1 Fib1C-KO2 Fib1C-KO3 Fib1C-WT1 Fib1C-WT2
> Fib1C-WT3
>
> 1415768_a_at  8.240705  8.332744  8.176031  8.949155
> 8.913745  8.858628
>
> 1415810_at    7.305646  7.565421  7.219027  6.027602
> 6.098046  5.857212
>
> 1415811_at    6.671428  6.625956  6.554472  5.264805
> 5.554093  5.674547
>
> and so on....
>
>
>
> Thank you,
> Saurin
>
>
>
>
> --- Wolfgang Huber <huber at ebi.ac.uk> wrote:
>
>> 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
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >
>>
>>
>> -------------------------------------
>> 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
>> -------------------------------------
>>
>
>
>
>
>
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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