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
--
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.
You received this message because you are subscribed to the Google Groups
aroma.affymetrix group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
--
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.
You received this message because you are subscribed to the Google Groups
aroma.affymetrix group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
