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Question: Processing data from Illumina HumanCNV370-Quad chips
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gravatar for Steven McKinney
9.3 years ago by
Steven McKinney310 wrote:
Hi all, 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 I'm pouring through documentation, but as yet have not seen references to this chip type, so am wondering if I just don't have things set up just right as yet, or whether the current software is not yet ready to deal with data from this chip type. I don't see any references to this chip type in the mail archives. Any feedback appreciated. Best 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
ADD COMMENTlink modified 9.2 years ago • written 9.3 years ago by Steven McKinney310
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gravatar for Oosting, J. PATH
9.3 years ago by
Oosting, J. PATH550 wrote:
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("S ample_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 [[alternative HTML version deleted]]
ADD COMMENTlink written 9.3 years ago by Oosting, J. PATH550
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gravatar for Steven McKinney
9.2 years ago by
Steven McKinney310 wrote:
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@lumc.nl [mailto:J.Oosting@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("S ample_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
ADD COMMENTlink written 9.2 years ago by Steven McKinney310
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