Hi,

I am using the `genotype.Illumina` function from `clrmm` package. This is my code:

library(crlmm)
library(ff)
cnSet <- genotype.Illumina(sampleSheet=samplesheet,
                           arrayNames=arrayNames,
                           arrayInfoColNames=arrayInfo,
                           cdfName="human610quadv1b",
                           batch=batch)

Now when running this function, a lot of .ff files are created in the working directory and it is causing a problem because after a point when the number of files are large, I get an error: 

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

Error in ff(initdata = initdata, vmode = vmode, dim = dim, pattern = file.path(ldPath(),  : 

  write error

Is there an option where you can circumvent the creation of these files?

Thanks!

Are you solving the problem now? I encountered the same problem  ：）