Illumina SNParray reading with beadarraySNP Bioconductor package

Question

[obsteter.jana]

Hi,

I am trying to read my raw Illumina SNP data (Illumina Bovine 50K v2) into R. I am using Bioconductor's beadarraySNP package. When using read.SnpSetIllumina() function I want to add Illumina's manifest file in order to convert raw report file to SnpSetIllumina object, but I am struggling with what format the manifest file has to be in and how to specify it in the command

read.SnpSetIllumina(Sample_Map2Samplesheet("Sample_Map.txt", reportfile="FinalReport.txt")

It works great if I use nochecks=T option but then it returns Multiset object. Any help or suggestions how to best read and process Illumina raw files would be greatly appreciated :)

Thanks!

Answer 1

[Jan Oosting]

You really should read the error message that is displayed when you run read.SnpSetIllumina()

It informs you which fields are missing from the reportfile.

Manifest files are not integrated into the result object. Only the data available in the reporrtfile.

If you don't need the copy-number functionality of the package, the multiset object will probably be good enough for you.