[BioC] Processing data from Illumina HumanCNV370-Quad chips
smckinney at bccrc.ca
Tue Nov 25 05:30:24 CET 2008
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
> ccld <- read.SnpSetIllumina(samplesheet = "ccl_CNV370SampleSheet_8samples.csv",
+ reportfile = "ccl_FinalReport_2.txt")
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!
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
675 West 10th Ave, Floor 4
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
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")
>Has anyone processed data from Illumina
>HumanCNV370-Quad chips using Bioconductor
>or other open source software?
>I've started attempts to read data using
>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
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