[BioC] Oligo package, possible bug in paCalls

[James Perkins]

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