[BioC] Error: All CEL files must be of the same type when running CRLMM

[Henrik Bengtsson]

The chip types are identical - it is only the CDFs that differ.
Assuming the assays didn't change too much you should be able to
analyze them together.  A workaround is to create a copy of the "old"
CEL files with an updated chip type, e.g.

  library("affxparser");
  convertCel(filename, outFilename, newChipType="Mapping250K_Nsp");

/Henrik

On Sat, Jun 27, 2009 at 8:55 PM, Vincent
Carey<stvjc at channing.harvard.edu> wrote:
> Examining the platform metadata for GSE9222 we can see that there are
> "early access" Nsp arrays
> and standard 250k Nsp.  I would think that your best bet is to use
> samples that are clearly from platform
> GPL3718.
>
> On Sat, Jun 27, 2009 at 6:32 PM, <mcoyne at boninc.com> wrote:
>>  I downloaded a number of SNP 500K data from GEO to run with CRLMMM.
>> The following CEL files specified by GEO as NspI files.
>>  > fulFileNames
>>  [1] "/Users/pcoyne/B_Cluster_DBased/GSE9222/NspI/GSM234158.CEL"
>>  [2] "/Users/pcoyne/B_Cluster_DBased/GSE9222/NspI/GSM234160.CEL"
>>  [3] "/Users/pcoyne/B_Cluster_DBased/GSE9222/NspI/GSM234162.CEL"
>>  > crlmm (fulFileNames,outputDir,verbose=TRUE,
>> pkgname="pd.mapping250k.nsp")
>>  chips
>>  Mapping250K_Nsp      Mendel_Nsp
>>               2               1
>>  Error in justCRLMMv3(filenames, outdir, batch_size = batch_size,
>> recalibrate = recalibrate,  :
>>   All the CEL files must be of the same type.
>>  > sessionInfo()
>>  R version 2.9.0 (2009-04-17)
>>  i386-apple-darwin8.11.1
>>  locale:
>>  en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>  attached base packages:
>>  [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>  other attached packages:
>>  [1] pd.mapping250k.sty_0.4.1 pd.mapping250k.nsp_0.4.1 RSQLite_0.7-1
>>
>>  [4] DBI_0.2-4                oligo_1.8.1
>> preprocessCore_1.6.0
>>  [7] oligoClasses_1.6.0       Biobase_2.4.1
>>  loaded via a namespace (and not attached):
>>  [1] affxparser_1.16.0 affyio_1.12.0     Biostrings_2.12.7
>> IRanges_1.2.3
>>  [5] splines_2.9.0
>>  >
>>  Question 1:  What is Mendel_nsp?  It looks like one of the file is
>> Mendel_nsp
>>  Question 2:  Is this an error that I can by pass with CRLMM and how?
>> or is it an error that I should report to GEO for fixitng?
>>  Thanks
>>  My Coyne
>>  mcoyne at boninc.com
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>
>
>
> --
> Vincent Carey, PhD
> Biostatistics, Channing Lab
> 617 525 2265
>
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