[BioC] Processing data from Illumina HumanCNV370-Quad chips

[Steven McKinney]

Hi Jan,

Thanks very much for these guidelines.
Getting the annotations into the final report
via BeadStudio, plus the sample sheet, yielded
a successful pair of files to get the data
read in.

> ccld <- read.SnpSetIllumina(samplesheet = "ccl_CNV370SampleSheet_8samples.csv",
+                             reportfile = "ccl_FinalReport_2.txt")
Warning message:
In read.SnpSetIllumina(samplesheet = "ccl_CNV370SampleSheet_8samples.csv",  :
  OPA info file could not be (uniquely) identified for HumanCNV370-Quadv3_C Using chromosomal position from report file

We will worry about the OPA file another day!
(Any suggestions?)

Thanks much


Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney +at+ bccrc +dot+ ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada




-----Original Message-----
From: J.Oosting at lumc.nl [mailto:J.Oosting at lumc.nl]
Sent: Thu 11/13/2008 11:49 PM
To: Steven McKinney; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] Processing data from Illumina HumanCNV370-Quad chips
 
Hi Steven,
 
If you have access to Beadstudio, probably the easiest way to get Illumina SNP data loaded in beadarraySNP is the following
- Do genotyping of your data in Beadstudio
- Create a final report (From the Analysis->Reports menu) that contains at least the fields 'SNP Name', 'Sample ID', 'GC Score', 'Allele1 - AB', 'Allele2 - AB', 'GT Score', 'X Raw',  'Y Raw', 'Chr' and 'Position'. Any other fields you select here will also be imported. Be sure to enable the checkbox to create a 'Sample MAP'
- Now you can use the sample_map.txt file as a samplesheet by using the Sample_Map2Samplesheet() function
- load the data: mydata<-read.SnpSetIllumina(Sample_Map2Samplesheet("Sample_Map.txt"),reportfile="reportfile.txt")
 
Jan

>Has anyone processed data from Illumina
>HumanCNV370-Quad chips using Bioconductor
>or other open source software?
>
>I've started attempts to read data using
>beadarraySNP
>but have not had luck yet.

>> SNPdata <- read.SnpSetIllumina("Gulisa_CNV370SampleSheet_8samples.csv")
>Error in read.SnpSetIllumina("Gulisa_CNV370SampleSheet_8samples.csv") :
>  Sample sheet error, column(s) Sentrix_Position, Pool_ID, Sentrix_ID are not available
>Steven McKinney