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hansenlab / minfi

Devel repository for minfi
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EstimateCellCounts with EPIC V2 data #266

Open kimberzhu opened 9 months ago

kimberzhu commented 9 months ago

Hi, Im running into issues when using EstimateCellCounts to deconvolute blood cell types when using EPICV2 array data.

Running: 

cellCounts <- estimateCellCounts(rgSet)

Gives me this error:

Error in .convertArray_450k_epic(rgSet = object, outType = outType, verbose = verbose) : 
  .is450k(rgSet) || .isEPIC(rgSet) is not TRUE

Is it because of my array/annotation being EPIC V2? Heres some info about my rgSet:

rgSetFlt class: RGChannelSet dim: 1105209 219 metadata(0): assays(2): Green Red rownames(1105209): 1600157 1600179 ... 99810982 99810990 rowData names(0): colnames(219): 207925050049_R07C01 207882990112_R05C01 ... 207865030003_R05C01 207865030077_R04C01 colData names(15): Sample_Name Sample_Plate ... Basename filenames Annotation array: IlluminaHumanMethylationEPICv2 annotation: 20a1.hg38

Thanks in advance for any help!

zwang072005 commented 6 months ago

Have you solve your problem? I have the same issure .