Looks like there was some problems reading the file in on my end, some
chromosomes didn't make it in probably from a preprocessing step on my end.
I'll let you know if I can't rectify.

Thanks again for the help,

Sam


On Thu, May 30, 2013 at 4:43 PM, Stephanie M. Gogarten <
sdmorris@u.washington.edu> wrote:

> Hi Sam,
>
> I need to add a more informative error message - the problem is that no
> valid BAF values are reaching the call to CNA (baf.dat is NULL).  This
> could happen if the values of snp.ids or chrom.ids are invalid - these
> should all be integer values matching the contents of snpID and chromosome
> in the netCDF file.  What values are you using for these arguments?
>
> You will need to have LRR in the intensity NetCDF file.  A portion of the
> code downstream from the error you're getting uses LRR to filter potential
> anomalies.
>
> Stephanie
>
>
> On 5/30/13 12:30 PM, Sam Rose wrote:
>
>> Thank you for your previous help Stephanie.
>>
>> I am afraid I have another problem I can't seem to work out.
>>
>> I have gotten as far as reading in the BAlleleFreq and Geno files into
>> their respective ncdf formats. I only have the baf data in the intensity
>> ncdf file, do I need LRR too? When I run the anomDetectBAF() function it
>> gives me this error:
>>
>>  > anom <- anomDetectBAF(blData, genoData, scan.ids=scan.ids,
>> chrom.ids=chrom.ids, snp.ids=snp.ids, centromere=centromeres.hg19)
>> Error in CNA(as.vector(baf.dat), chr, index, data.type = "logratio",
>> sampleid = snum) :
>>    genomdat must be numeric
>>
>> I have checked and the data that I put in to the genotype data file was
>> numeric and present as well as the baf data. I'm wondering if you have
>> seen this error before and may potentially know what I can do to rectify?
>>
>> Thanks,
>> Sam
>>
>>
>> On Wed, Apr 24, 2013 at 12:01 AM, Stephanie M. Gogarten
>> <sdmorris@u.washington.edu <mailto:sdmorris@u.washington.**edu<sdmorris@u.washington.edu>>>
>> wrote:
>>
>>     Hi Sam,
>>
>>     Section 2 of the vignette "GWAS Data Cleaning" contains an example
>>     of how to import raw illumina data of exactly this type into
>>     GWASTools. The example data is contained in the package "GWASdata."
>>
>>     If you have any further questions after reading the vignette, please
>>     cc the bioconductor mailing list (bioconductor@r-project.org
>>     <mailto:bioconductor@r-**project.org <bioconductor@r-project.org>>).
>>
>>
>>     Section 7 may also be of use to you, as it deals with chromosome
>>     anomaly detection.
>>
>>     best wishes,
>>     Stephanie
>>
>>
>>     On 4/23/13 7:54 PM, Sam Rose wrote:
>>
>>         Hi Stephanie,
>>
>>         My name is Sam Rose and I am contacting you the GWASTools package
>> in
>>         Bioconductor of which it says you are the maintainer.
>>
>>         I am trying to use the package to call mosaic CNVs in my samples
>> and
>>         can't seem to get it to work.
>>
>>         I'm wondering if you have an example of the raw illumina data to
>>         put in
>>         there, and maybe examples of some of the things required in the
>>         'ncdfAddData' command (i.e. sample column, col.nums). I have
>>         created the
>>         shell ncdf file, but beyond that the headers and data formats
>>         seem to be
>>         giving me trouble so I just though I would ask.
>>
>>         Our Illumina raw data files look like this:
>>         SNP_NameChromosomePositionGC__**_ScoreAllele1_-_TopAllele2_-__**
>> _TopAllele1_-_ABAllele2_-___**ABXYRaw_XRaw_YR_IlluminaTheta_**
>> __IlluminabAllele_FreqLog_R___**Ratio_IlluminaR_TrigTheta___**
>> TrigLog_R_Ratio_Trig
>>         rs44772121720170.__**38423407AAAA0.__**393692269026780450.__**
>> 0250181864147452338333240.__**41871045544152570.__**040401312884379780.__
>> **006063504097364059-0.__**6120798296992830.__**394486390567453940.__**
>> 06346223387647508-0.__**6182450719587295
>>
>>
>>         Thanks for your help,
>>
>>         Sam
>>
>>         --
>>         -----
>>         *Sam Rose, Stanley Center Research Associate II
>>
>>         Stanley Center for Psychiatric Research, The Broad Institute
>>         7 Cambridge Center, Cambridge, MA 02142*
>>         617.714.7853, srose@broadinstitute.org
>>         <mailto:srose@broadinstitute.**org <srose@broadinstitute.org>>
>>         <mailto:srose@broadinstitute._**_org
>>         <mailto:srose@broadinstitute.**org <srose@broadinstitute.org>>>
>>
>>
>>
>>
>>
>> --
>> -----
>> *Sam Rose, Stanley Center Research Associate II
>> Stanley Center for Psychiatric Research, The Broad Institute
>> 7 Cambridge Center, Cambridge, MA 02142*
>> 617.714.7853, srose@broadinstitute.org <mailto:srose@broadinstitute.**org<srose@broadinstitute.org>
>> >
>>
>>


-- 
-----
*Sam Rose, Stanley Center Research Associate II
Stanley Center for Psychiatric Research, The Broad Institute
7 Cambridge Center, Cambridge, MA 02142*
617.714.7853, srose@broadinstitute.org

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