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> 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).
>
> 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>
>> >
>>
>>


-- 
-----
*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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