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Hi Benilton,
I?m 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(?Test.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. I?m
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
