[BioC] oligo package problem reading HuGene arrays

[Rob Dunne]

Hi List,

I am having a problem reading HuGene 1.0 arrays with the oligo package.

library(oligo)
read.celfiles(filenames=filenames)
# Could not open file 
~/Downloads/SSA/original/CC_Black_(HuGene-1_0-st-v1).CEL

Looking inside read.celfiles, it seems that the problem may start with 
getCelChipType

oligo:::getCelChipType(filenames[1],TRUE)
Error in read.celfile.header(x) :
   Could not open file 
~/Downloads/SSA/original/CC_Black_(HuGene-1_0-st-v1).CEL

changing the useAffyio to FALSE seems to work.
oligo:::getCelChipType(filenames[1],useAffyio=FALSE)
[1] "HuGene-1_0-st-v1"

However the useAffyio option has been removed from read.celfiles and 
changing read.celfiles at this point
just moves the problem further down into the function.


Bye
Rob

 > sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-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=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] pd.hugene.1.0.st.v1_3.6.0 RSQLite_0.11.2
[3] DBI_0.2-5                 oligo_1.20.4
[5] 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_1.4.9 Biostrings_2.24.1
  [7] bit_1.1-9             codetools_0.2-8 ff_2.2-10
[10] foreach_1.4.0         IRanges_1.14.4 iterators_1.0.6
[13] preprocessCore_1.18.0 splines_2.15.2 stats4_2.15.2
[16] tools_2.15.2          zlibbioc_1.2.0




-- 
Rob Dunne         Fax: +61 2 9325 3200     Tel: +61 2 9325 3263
CSIRO Mathematical and Information Sciences     +61 2 9325 3100
Locked Bag 17, North Ryde, New South Wales, Australia, 1670
http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au

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