[BioC] oligo package - Unable to read HT-U133A CEL files

[Steve Piccolo]

Hi Benilton,

I¹m using the oligo package to try to read CEL files from the Affymetrix
HT-U133A platform. These arrays rely on the pd.ht.hg.u133a annotation
package. When I use the following command, I get an error:

> x = read.celfiles(³Test.CEL")
Platform design info loaded.
Reading in : Test.CEL
Error in data.frame(exprs = filenames, dates = dates) :
  arguments imply differing number of rows: 1, 0


I tried the previous version of oligo (1.26.6), and it seems to work just
fine. But the latest version (1.28.0) is giving me this error. I do not
seem to be getting the same error for other Affy array types. I¹m seeing
the same behavior on two different computers. Below is the session info
for one of them.


R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C


attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base     


other attached packages:
 [1] pd.ht.hg.u133a_1.10.0 RSQLite_0.11.4        DBI_0.2-7
 [4] SCAN.UPC_2.6.0        sva_3.10.0            mgcv_1.7-29
 [7] nlme_3.1-117          corpcor_1.6.6         foreach_1.4.2
[10] affyio_1.32.0         affy_1.42.2           GEOquery_2.30.0
[13] oligo_1.28.0          Biostrings_2.32.0     XVector_0.4.0
[16] IRanges_1.22.6        oligoClasses_1.26.0   Biobase_2.24.0
[19] BiocGenerics_0.10.0   BiocInstaller_1.14.2


loaded via a namespace (and not attached):
 [1] affxparser_1.36.0     bit_1.1-12            codetools_0.2-8
 [4] compiler_3.1.0        ff_2.2-13             GenomeInfoDb_1.0.2
 [7] GenomicRanges_1.16.3  grid_3.1.0            iterators_1.0.7
[10] lattice_0.20-29       MASS_7.3-33           Matrix_1.1-3
[13] preprocessCore_1.26.0 RCurl_1.95-4.1        splines_3.1.0
[16] stats4_3.1.0          tools_3.1.0           XML_3.98-1.1
[19] zlibbioc_1.10.0



Thanks,
-Steve