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,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]]

