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

[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
> -------------------------------------
>