Hi Steve, it's fixed on oligo 1.28.2, which should appear online during the
next few days. Thank you very much, benilton


2014-05-08 17:35 GMT-03:00 Steve Piccolo <stephen.piccolo@hsc.utah.edu>:

> 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
>
>
>


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Benilton Carvalho
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