[BioC] Problem reading Cel files - Oligo Package

[Atul]

Hi All,

I am trying to read four *.Cel files into oligo and getting this error:

 > celFiles <- list.celfiles()
 > celFiles
[1] "Iris.CEL" "Liv1.CEL" "Liv2.CEL" "Liv3.CEL"
 > AF_data = read.celfiles(celFiles)
All the CEL files must be of the same type.
Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE

Then I tried reading files separately (one by one) and found that one 
sample (Iris.CEL) shows annotation package as 'pd.huex.1.0.st.v1' while 
rest (Liv1,Liv2,Liv3) are 'pd.huex.1.0.st.v2'. I checked on GEO and 
found that though all the samples are from different studies but were 
generated using same chip - Human Exon 1.0 ST Arrays and the one which 
is giving error (Iris.cel )have 'HuEx-1_0-st-v2.r2.dt1.hg18.core.ps' 
mentioned under data processing description, that means it is also 
version2 of HuEx 1.0ST.

So I explicitly mentioned annotation package 'pd.huex.1.0.st.v2' instead 
of the one recognized by oligo ('pd.huex.1.0.st.v1') and file is read 
without any problem:

 > celFiles <- list.celfiles()
 > celFiles
[1] "Iris.CEL"
 > AF_data = read.celfiles(celFiles,pkgname='pd.huex.1.0.st.v2')
Platform design info loaded.
Reading in : Iris.CEL

But if I add other files and try same thing, than the error is back:
 > celFiles <- list.celfiles()
 > celFiles
[1] "Iris.CEL" "Liv1.CEL" "Liv2.CEL" "Liv3.CEL"
 > AF_data = read.celfiles(celFiles,pkgname='pd.huex.1.0.st.v2')
All the CEL files must be of the same type.
Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE


Can anybody please tell me why annotation package for Iris.cel which is 
from HuEx 1.0ST v2 (from NCBI GEO description) is recognized as 
'pd.huex.1.0.st.v1'? If explicitly mention package name 
pd.huex.1.0.st.v2 and try to read Iris.cel alone, it works. But if read 
with other cel files with same annotation (pd.huex.1.0.st.v2) it gives 
error??

NCBI GEO ID:
Iris.cel - GSM1008547
Liv1/2/3 - GSM486433/GSM486434/GSM486435

Awaiting help.

AK


Session Info:

 > sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C LC_TIME=en_US.UTF-8        
LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
  [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=C LC_NAME=C                  
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   
base

other attached packages:
[1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.4 DBI_0.2-7               
oligo_1.24.2 Biobase_2.20.1          oligoClasses_1.22.0
[7] BiocGenerics_0.6.0

loaded via a namespace (and not attached):
  [1] affxparser_1.32.3     affyio_1.28.0 BiocInstaller_1.10.1  
Biostrings_2.28.0     bit_1.1-10 codetools_0.2-8
  [7] ff_2.2-11             foreach_1.4.0 GenomicRanges_1.12.4  
IRanges_1.18.1        iterators_1.0.6 preprocessCore_1.22.0
[13] splines_3.0.1         stats4_3.0.1 tools_3.0.1           
zlibbioc_1.6.0