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

[Vincent Carey]

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