crlmm: Does it support Illumina BeadChip platform HumanCore-24v1-0_A
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enriquev • 0
@enriquev-11235
Last seen 4.8 years ago

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'

 

cnv cnvtools crlmm • 771 views
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