On Friday, September 14, 2012, Mike wrote:
> To clarify, one segment ends at 29837188, the next starts at 29837188.
>
> On Friday, September 14, 2012 5:10:00 PM UTC-4, Mike wrote:
>>
>> Henrik,
>>
>> I am getting errors when running the RAE algorithm from MSKCC due to the
>> fact that there are multiple probes that map to the same locus. It throws
>> off the count of the algorithm when there are segments that start and end
>> at the same locus with different CN calls. This causes the algorithm to
>> error out because I end up with vectors of different lengths.
>>
>
I see (seems to be a design bug of RAE then).
>> Can you suggest a reasonable work around? Only use SNP probes for these
>> locations? Take median CN for probes mapping to same location?
>>
>
Either works. Simplest would be to drop non-polymorphic ("CN") loci that
have same locations as other SNPs/CN loci. In the end of the day it won't
matter much what you do, because this only affects a teeny fraction of the
data you have.
/Henrik
>> Thanks,
>> Mike
>>
>> On Friday, September 14, 2012 5:00:42 PM UTC-4, Henrik Bengtsson wrote:
>>>
>>> On Fri, Sep 14, 2012 at 1:57 PM, Mike <michael...@gmail.com> wrote:
>>> > I am using aroma.affymetrix for pre-processing of data for CNV
>>> analysis.
>>> > Briefly, I normalize and estimate copy number with CRMAv2. I use the
>>> > calculated copy number along with the chromosomal locations from the
>>> ugp
>>> > file to run CBS using segment from the DNAcopy package. Then I
>>> analyze the
>>> > segmented copy number calls with downstream software like RAE from
>>> MSKCC.
>>> >
>>> > I am analyzing data collected on the GWS6 platform. I am getting
>>> errors
>>> > when multiple probes map to the same genomic location. For example,
>>> probe
>>> > SNP_A-8462292 and probe CN_1173216 both map to chromosome 6 locus
>>> 29837188.
>>> > Is this behavior expected? Is there a work around for this issue?
>>>
>>> Yes, for some probes the Affymetrix annotation happens to have the
>>> exact same genomic location. The DNAcopy implementation of CBS is
>>> what generates those warnings (they are *not* errors). They will not
>>> cause an issue.
>>>
>>> /Henrik
>>>
>>> >
>>> > Thanks,
>>> > Mike
>>> >
>>> > --
>>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest
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>>> >
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>>
--
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