I am trying to run crlmm package function genotype.Illumina to get CNSet object for my illumina data from HumanCore-24v1-0_A BeadChips. But this chip name is not listed under the supported platform list in crlmm package. How do I go about using crlmm?
The only supported platforms are:
krlmm.supported = c("humanomni1quadv1b", "humanomni25quadv1b",
"humanomni258v1a", "humanomni258v1p1b", "humanomni5quadv1b",
"humanexome12v1p2a", "humanomniexpexome8v1p1b")
crlmm.supported = c("human1mv1c", "human370v1c", "human650v3a",
"human610quadv1b", "human660quadv1a", "human370quadv3c",
"human550v3b", "human1mduov3b", "humanomni1quadv1b",
"humanomniexpress12v1b", "humanimmuno12v1b", "humancytosnp12v2p1h",
"humanomniexpexome8v1p1b")
# Error message from the codes I am using below.
> cnSet <- genotype.Illumina(sampleSheet=csvFile,
+ arrayNames=arrayNames,
+ arrayInfoColNames=arrayInfo,
+ cdfName="humanCore24v1")
Error in genotype.Illumina(sampleSheet = csvFile, arrayNames = arrayNames, :
humanCore24v1 platform not supported by crlmm. Consider setting call.method='krlmm'
> cnSet <- genotype.Illumina(sampleSheet=csvFile,
+ arrayNames=arrayNames,
+ arrayInfoColNames=arrayInfo,
+ call.method='krlmm',
+ cdfName="humanCore24v1")
Error in genotype.Illumina(sampleSheet = csvFile, arrayNames = arrayNames, :
humanCore24v1 platform not supported by krlmm. Consider setting call.method='crlmm'