Crlmm package
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@khadeeja-ismail-4711
Last seen 5.6 years ago
Dear All, I'm trying to preprocess data from Illumina's GoldenGate assay, using the crlmm package. I tried to follow the userguide but keeps getting an error after the quantile normalization step. My output is as shown below. > cnSet <- genotype.Illumina(sampleSheet=samplesheet,arrayNames=arrayN ames,arrayInfoColNames=arrayInfo,cdfName="human370v1c",batch=batch) Instantiate CNSet container. ....... Loading chip annotation information. Quantile normalizing 278 arrays by 12 strips. |==================================================================== ==| 100% Loading snp annotation and mixture model parameters. Calibrating 278 arrays.   | |   0%Error in chol.default(crossprod(sweep(matS, 1, z[, 1], FUN = "*"), matS)) :   the leading minor of order 1 is not positive definite My SampleSheet is as shown belowSample_ID, Sample_Name, Sample_Plate, Sample_Well, SentrixBarcode_A, Position,        Type, SentrixPosition_A ABC.142,    ABC.142,         NA, NA,                 6924968003,          R01C01,       RNA,       A ABC.143.    ABC.143,         NA,                NA, 6924968003,          R01C02,       RNA,       A ABC.896,    ABC.896,         NA, NA                  6924968003,          R01C03,       DNA,       A Would be great if someone could point out the cause of this error. Also, is there any other packages I can use to preprocess and genotype starting from iDat files? Thanks, Khadeeja [[alternative HTML version deleted]]
SNP Annotation Normalization crlmm SNP Annotation Normalization crlmm • 1.0k views
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Matthew Ritchie ▴ 1000
@matthew-ritchie-650
Last seen 5 months ago
Australia
Dear Khadeeja, The crlmm package can only be used to process and genotype data from Infinium SNP chips. GoldenGate arrays are not supported. I'm not aware of any other packages in Bioconductor for calling genotypes for Illumina arrays from IDAT files. Your best bet will be to use the calls produced by Illumina's software. I hope this helps. Best wishes, Matt > Dear All, > > I'm trying to preprocess data from Illumina's GoldenGate assay, using the > crlmm package. I tried to follow the userguide but keeps getting an error > after the quantile normalization step. My output is as shown below. > > > > >> cnSet <- >> genotype.Illumina(sampleSheet=samplesheet,arrayNames=arrayNames,arr ayInfoColNames=arrayInfo,cdfName="human370v1c",batch=batch) > Instantiate CNSet container. > ....... > Loading chip annotation information. > Quantile normalizing 278 arrays by 12 strips. > ? > |================================================================== ====| > 100% > Loading snp annotation and mixture model parameters. > Calibrating 278 arrays. > ? |????????????????????????????????????????????????????????????????????? > |?? 0%Error in chol.default(crossprod(sweep(matS, 1, z[, 1], FUN = "*"), > matS)) : > ? the leading minor of order 1 is not positive definite > > > My SampleSheet is as shown belowSample_ID, Sample_Name, Sample_Plate, > Sample_Well, SentrixBarcode_A, Position,??????? Type,????? > SentrixPosition_A > ABC.142,??? ABC.142,???????? NA,??????????????? > NA,???????????????? 6924968003,????????? R01C01,?????? RNA,?????? A > ABC.143.??? ABC.143,???????? NA,??????????????? NA,???????????????? > 6924968003,????????? R01C02,?????? RNA,?????? A > ABC.896,??? ABC.896,???????? NA,??????????????? > NA????????????????? 6924968003,????????? R01C03, ?? ?? DNA,?????? A > > > > > Would be great if someone could point out the cause of this error. > Also, is there any other packages I can use to preprocess and genotype > starting from iDat files? > > Thanks, > Khadeeja ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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