Thanks for the speedy fix! I downloaded from svn and so far it seems to be
working ok.

Cheers,

Jim

On 4 July 2012 17:49, Benilton Carvalho <beniltoncarvalho@gmail.com> wrote:

> this has been addressed on oligo 1.20.4, which should appear online soon. b
>
> On 4 July 2012 12:01, Benilton Carvalho <beniltoncarvalho@gmail.com>
> wrote:
> > thanks for the report, will get back to you asap. b
> >
> > On 4 July 2012 11:58, James Perkins <j.perkins@ucl.ac.uk> wrote:
> >> Dear Benilton,
> >>
> >> I had a problem running paCalls() from the oligo package, specifically
> I got:
> >>
> >> Error in dimnames(res) <- list(fid, sampleNames(x)) :
> >>   length of 'dimnames' [1] not equal to array extent
> >>
> >>>      if (require(oligoData) & require(pd.huex.1.0.st.v2)){
> >> +        data(affyExonFS)
> >> +        ## Get only 2 samples for example
> >> +        dabgP = paCalls(affyExonFS[, 1:2])
> >> +        dabgPS = paCalls(affyExonFS[, 1:2], "PSDABG")
> >> +        head(dabgP) ## for probe
> >> +        head(dabgPS) ## for probeset
> >> +      }
> >> Loading required package: oligoData
> >> Loading required package: pd.huex.1.0.st.v2
> >> Loading required package: RSQLite
> >> Loading required package: DBI
> >> Computing DABG calls... Error in dimnames(res) <- list(fid,
> sampleNames(x)) :
> >>   length of 'dimnames' [1] not equal to array extent
> >>> traceback()
> >> 4: paFun(object)
> >> 3: .local(object, method, ..., verbose)
> >> 2: paCalls(affyExonFS[, 1:2]) at #4
> >> 1: paCalls(affyExonFS[, 1:2]) at #4
> >>> sessionInfo()
> >> R version 2.15.0 (2012-03-30)
> >> Platform: x86_64-unknown-linux-gnu (64-bit)
> >>
> >> locale:
> >>  [1] LC_CTYPE=en_US             LC_NUMERIC=C
> >>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> >>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
> >>  [7] LC_PAPER=C                 LC_NAME=C
> >>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> other attached packages:
> >> [1] pd.huex.1.0.st.v2_3.6.0 RSQLite_0.11.1          DBI_0.2-5
> >> [4] oligoData_1.6.0         oligo_1.20.3            oligoClasses_1.18.0
> >>
> >> loaded via a namespace (and not attached):
> >>  [1] affxparser_1.28.1     affyio_1.24.0         Biobase_2.16.0
> >>  [4] BiocGenerics_0.2.0    BiocInstaller_1.4.7   Biostrings_2.24.1
> >>  [7] bit_1.1-8             codetools_0.2-8       ff_2.2-7
> >> [10] foreach_1.4.0         IRanges_1.14.4        iterators_1.0.6
> >> [13] preprocessCore_1.18.0 splines_2.15.0        stats4_2.15.0
> >> [16] tools_2.15.0          zlibbioc_1.2.0
> >>>
> >>
> >> I can confirm it worked as expected with R-2.13.0, so I assume this is
> a bug?
> >>
> >> Many thanks,
> >>
> >> Jim
> >> --
> >> James Perkins
> >> Institute of Structural and Molecular Biology
> >> Division of Biosciences
> >> University College London
> >> Gower Street
> >> London, WC1E 6BT
> >> UK
> >>
> >> email: j.perkins@ucl.ac.uk
> >>
> >> _______________________________________________
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> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
James Perkins
Institute of Structural and Molecular Biology
Division of Biosciences
University College London
Gower Street
London, WC1E 6BT
UK

email: j.perkins@ucl.ac.uk

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