Hi everyone, 

I am using the genotype.Illumina function from crlmm. The following is my code and the error that I am getting:

> head(samplesheet)

            SampleID SentrixPosition SentrixBarcode                         Array
TARGET-30-PAAPFA-10A    1906277330_A     1906277330    Illumina.com:HumanHap550v3 
TARGET-30-PACRYY-10A    1906277899_A     1906277899    Illumina.com:HumanHap550v3 
TARGET-30-PACUGP-10A    1870075248_A     1870075248    Illumina.com:HumanHap550v3 
TARGET-30-PADENF-10A    1906277855_A     1906277855    Illumina.com:HumanHap550v3 
TARGET-30-PADIEY-10A    1870147515_A     1870147515    Illumina.com:HumanHap550v3 
TARGET-30-PADIRB-10A    1906277047_A     1906277047    Illumina.com:HumanHap550v3           

> head(arrayNames)

[1] "1906277330_A"
[2] "1906277899_A"
[3] "1870075248_A"
[4] "1906277855_A"
[5] "1870147515_A"
[6] "1906277047_A"

> head(arrayInfo)

$barcode
[1] "SentrixBarcode"
$position
[1] "SentrixPosition"

> head(batch)

[1] "1" "1" "1" "1" "1" "1"

# run genotype.Illumina function
cnSet <- genotype.Illumina(sampleSheet=samplesheet,
                           arrayNames=arrayNames,
                           arrayInfoColNames=arrayInfo,
                           cdfName="human550v3b",
                           batch=batch) 

Instantiate CNSet container.
path arg not set.  Assuming files are in local directory, or that complete path is provided
Initializing container for genotyping and copy number estimation
Processing sample stratum 1 of 1
path arg not set.  Assuming files are in local directory, or that complete path is provided

Loading chip annotation information.
Quantile normalizing 92 arrays by 10 strips.
  |======================================================================| 100%
Loading snp annotation and mixture model parameters.
Calibrating 92 arrays.
  |=====================================================                 |  76%Error in chol.default(crossprod(sweep(matS, 1, z[, 1], FUN = "*"), matS)) : 
  the leading minor of order 1 is not positive definite
In addition: Warning messages:
1: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel],  :
  Chips are not of the same type.  Skipping 6110681250_R01C01_Grn.idat and 6110681250_R01C01_Red.idat
2: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel],  :
  Chips are not of the same type.  Skipping 6184541022_R01C01_Grn.idat and 6184541022_R01C01_Red.idat
3: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel],  :
  Chips are not of the same type.  Skipping 6110681250_R02C01_Grn.idat and 6110681250_R02C01_Red.idat
4: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel],  :
  Chips are not of the same type.  Skipping 6110681250_R01C02_Grn.idat and 6110681250_R01C02_Red.idat
5: In readIdatFiles(sampleSheet = sampleSheet[sel, ], arrayNames = arrayNames[sel],  :
  Chips are not of the same type.  Skipping 6110681250_R02C02_Grn.idat and 6110681250_R02C02_Red.idat

So it does say that some chiops where skipped because they are not of the same type but what does the following error mean?

Error in chol.default(crossprod(sweep(matS, 1, z[, 1], FUN = "*"), matS)) : the leading minor of order 1 is not positive definite

Any help would be much appreciated. Thanks!

There were discrepancies in the chip types for some of the IDATs. Correcting that resolved the issue.