Hi.
On Fri, Apr 22, 2011 at 1:30 PM, HWright <wrig...@ohsu.edu> wrote:
> Hello; I'm quite new to analysis of the CNV/SNP chips and totally new
> to AROMA, so I apologize if this is an obvious question, but I'm
> attempting to use AROMA to step through the CRLMM genotyping vignette
> on some 6.0 chips we have and am encountering the following error
> after the SNPRMA normalization:
>
> Error in list(`CrlmmModel(ces, tags = "*,oligo")` = <environment>,
> `throw("Cannot fit CRLMM model: Chip type to be supported: ",
> chipType)` = <environment>, :
>
> [2011-04-22 13:12:55] Exception: Cannot fit CRLMM model: Chip type to
> be supported: GenomeWideSNP_6
Unfortunately, fitting/running CRLMM in aroma.affymetrix on
GenomeWideSNP_6 is not supported/implemented.
>
> Are the 6.0s not supported for this in Affy? Do I need to use oligo to
> do this?
Yes, you need to use the oligo package for running CRLMM on GenomeWideSNP_6.
> Is this unnecessary and all this information would come out
> of a CRMA/ACNE analysis (we would like to get copy number as well for
> our analysis)?
If you want to do copy number analysis, I recommend that you use the
CRMAv2 preprocessing method which will give you locus-by-locus
copy-number estimates, which you then can pass on to segmentation
methods such as CBS. All this can be done within the aroma framework.
If you want *genotype calls* for your GenomeWideSNP_6, you need to use
oligo or another genotyping software. Note that genotype calls per se
are not needed for doing copy-number analysis/inference.
> I searched the group archives but most of the posts
> were from 2008 regarding not supporting CRLMM and since there was a
> vignette (albeit for 100k/500k) I wasn't sure if that was still the
> case.
Yes, that is still the case.
Hope this helps
Henrik
> Thanks...
>
> Hollis
>
> --
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>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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