[BioC] Oligo package, possible bug in paCalls

[Benilton Carvalho]

this has been addressed on oligo 1.20.4, which should appear online soon. b

On 4 July 2012 12:01, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
> 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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