crlmm : copy number and genotyping of Illumina data
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@abhishek-pratap-6167
Last seen 8.0 years ago
Hi All I am trying to use crlmm package for doing the genotyping and CNV analysis on a set ~200 samples genotyped on Illumina Omni5 array. I tried following the vignette (seems a bit dated) and got some errors(see below) http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst /doc/IlluminaPreprocessCN.pdf Also searching a bit more I found multiple functions in the code of crlmm like (genotype.Illumina, crlmmIlluminav2 etc) which seem to be doing similar stuff. Just wondering if someone can point me to the latest recipe(if any) of reading in the idat files (dual channel) and do the basic genotyping calling + copy number analysis. here is what I have done for a test case (5 arrays) > cnSet <- genotype.Illumina(sampleSheet = samplesheet[1:5,], + arrayNames = arrayNames[1:5], + arrayInfoColNames = list(barcode="SentrixBarcode_A", position="SentrixPosition_A"), + path = datadir, + copynumber = T, + batch = samplesheet$Sample_Group[1:5], + cdfName = "humanomni5quadv1b", + call.method = "krlmm", + verbose=T + ) Instantiate CNSet container. Initializing container for genotyping and copy number estimation reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5396_6298080101_R02 C01_Grn.idat reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5405_6298080103_R03 C01_Grn.idat reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5414_6298098003_R04 C01_Grn.idat reading /work/DAT_118__AML/Analysis/dset1/CNV/data/6431_8116121004_R03 C01_Grn.idat reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5423_6762372017_R01 C01_Grn.idat Processing sample stratum 1 of 1 Loading chip annotation information. Loading reference normalization information. Quantile normalizing 5 arrays, one at a time. |=================================================================== ============================| 100% Loading snp annotation and mixture model parameters. Calibrating 5 arrays. |========================================================= | 60% Error in quantile.default(M, c(1, 5)/6, names = FALSE) : missing values and NaN's not allowed if 'na.rm' is FALSE In addition: Warning messages: 1: In getProtocolData.Illumina(grnidats, sep = sep, fileExt = fileExt$green, : Chips are not of the same type. Skipping 6431_8116121004_R03C01_Grn.idat 2: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel], : Chips are not of the same type. Skipping 6431_8116121004_R03C01_Grn.idat and 6431_8116121004_R03C01_Red.idat Thanks! -Abhi
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Matthew Ritchie ▴ 1000
@matthew-ritchie-650
Last seen 2 days ago
Australia
Dear Abhi, You're using the appropriate function. Judging by the warning message, it looks like one of your samples is not like the others (i.e. sample 6431_8116121004 is not Omni5 version 1b). Maybe try leaving that one out and re-running? If that doesn't help, perhaps you could put the idat files for this test set of 5 arrays online so that I can take a closer look. Best wishes, Matt ----- Original Message ----- From: "Abhishek Pratap" <apratap@sagebase.org> To: bioconductor at r-project.org Sent: Tuesday, 18 February, 2014 11:01:38 AM Subject: [BioC] crlmm : copy number and genotyping of Illumina data Hi All I am trying to use crlmm package for doing the genotyping and CNV analysis on a set ~200 samples genotyped on Illumina Omni5 array. I tried following the vignette (seems a bit dated) and got some errors(see below) http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst /doc/IlluminaPreprocessCN.pdf Also searching a bit more I found multiple functions in the code of crlmm like (genotype.Illumina, crlmmIlluminav2 etc) which seem to be doing similar stuff. Just wondering if someone can point me to the latest recipe(if any) of reading in the idat files (dual channel) and do the basic genotyping calling + copy number analysis. here is what I have done for a test case (5 arrays) > cnSet <- genotype.Illumina(sampleSheet = samplesheet[1:5,], + arrayNames = arrayNames[1:5], + arrayInfoColNames = list(barcode="SentrixBarcode_A", position="SentrixPosition_A"), + path = datadir, + copynumber = T, + batch = samplesheet$Sample_Group[1:5], + cdfName = "humanomni5quadv1b", + call.method = "krlmm", + verbose=T + ) Instantiate CNSet container. Initializing container for genotyping and copy number estimation reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5396_6298080101_R02 C01_Grn.idat reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5405_6298080103_R03 C01_Grn.idat reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5414_6298098003_R04 C01_Grn.idat reading /work/DAT_118__AML/Analysis/dset1/CNV/data/6431_8116121004_R03 C01_Grn.idat reading /work/DAT_118__AML/Analysis/dset1/CNV/data/5423_6762372017_R01 C01_Grn.idat Processing sample stratum 1 of 1 Loading chip annotation information. Loading reference normalization information. Quantile normalizing 5 arrays, one at a time. |=================================================================== ============================| 100% Loading snp annotation and mixture model parameters. Calibrating 5 arrays. |========================================================= | 60% Error in quantile.default(M, c(1, 5)/6, names = FALSE) : missing values and NaN's not allowed if 'na.rm' is FALSE In addition: Warning messages: 1: In getProtocolData.Illumina(grnidats, sep = sep, fileExt = fileExt$green, : Chips are not of the same type. Skipping 6431_8116121004_R03C01_Grn.idat 2: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel], : Chips are not of the same type. Skipping 6431_8116121004_R03C01_Grn.idat and 6431_8116121004_R03C01_Red.idat Thanks! -Abhi ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}