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

[Carvalho, Benilton]

Using the argument:

pkgname="pd.mapping250k.nsp"

in crlmm() should get the job done by overriding the type check.

b

On 28/06/2009, at 14:18, "Henrik Bengtsson" <hb at stat.berkeley.edu>
wrote:

> 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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>
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