Question: Simple beadarraySNP analysis
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gravatar for Dmitri Mouradov
10.5 years ago by
Dmitri Mouradov20 wrote:
Hi all, Please bear with me as I am still new to beadarraySNP. I have a rather large SNP dataset (normal/tumor pairs) from iLLUMINA Human610-Quad beadchips. For the moment I am interested in doing simple copynumber/LOH analysis on the data set however I seem to get into trouble when plotting these, most likely as a result of "NA's" being introduced into the data set. I use BeadStudio to create a FinalReport with the following fields: 'SNP Name', 'Sample ID', 'GC Score', 'Allele1 - AB', 'Allele2 - AB', 'GT Score', 'X Raw', 'Y Raw', 'Chr' and 'Position' I also use it to create the sample_map file and manually add a "NorTum" column to it (this fixed some previous errors I was getting). The data reads in without errors using: read.SnpSetIllumina(Sample_Map2Samplesheet("Sample_Map.txt"), reportfile="FinalReport.txt") The normalization process runs with warnings. >SNPnrm <- normalizeBetweenAlleles.SNP(mydata4) Loading required package: limma > SNPnrm <- normalizeWithinArrays.SNP(SNPnrm, callscore = 0.8, relative = TRUE, fixed = FALSE, quantilepersample = TRUE) Warning message: In numericCHR(pData(featureData(object))[, "CHR"]) : NAs introduced by coercion > SNPnrm <- normalizeLoci.SNP(SNPnrm, normalizeTo = 2) Warning message: In atan2(y, x) : NaNs produced Finally when I try to plot the copyNumber things start going wrong. While the first sample seems to plot without any trouble the subsequent plots fail. >reportSamplesSmoothCopyNumber(SNPnrm, normalizedTo = 2, smooth.lambda = 4) Error in tmp.resp[1:ol] * portion : non-numeric argument to binary operator as well as 20 error messages stating: In .quantsmooth(intensities[i.s:i.e], smooth.lambda, tau, ... : data is all NA, result is NA I also can't run the copynumberConversion tool, with errors as follows: Error in `[.data.frame`(fData(object), , c("snpid", "IllCode", "CHR", : undefined columns selected Is there anything specific that I should check for or anything that I am doing in the wrong order. Any advice is more than welcome. Thank you in advace. Dmitri Mouradov Bioinformatician Ludwig Colon Cancer Initiative Laboratory PO Box 2008 Royal Melbourne Hospital VIC 3050, Australia Ph.: +61 (0) 3 93413155 Fax: +61 (0) 3 93413104 This communication is intended only for the named recipient and may contain information that is confidential, legally privileged or subject to copyright; the Ludwig Institute for Cancer Research Ltd does not waiver any rights if you have received this communication in error. The views expressed in this communication are those of the sender and do not necessarily reflect the views of the Ludwig Institute for Cancer Research Ltd. [[alternative HTML version deleted]]
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