[BioC] Oligo package, possible bug in paCalls

[Benilton Carvalho]

thanks for the report, will get back to you asap. b

On 4 July 2012 11:58, James Perkins <j.perkins at 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 at ucl.ac.uk
>
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