I'm using methylation file downloaded from GEO database, and tried to use champ.load to read methylation data (.idat).
However I was getting the following error :
"Error in champ.import(directory, arraytype = arraytype) : Error Match between pd file and Green Channel IDAT file."
I have checked the ChAMP code but was not able to find any ways to correct it.
I also tried loading various versions of csv files but was unsuccessful. I have posted one the the csv files below.
Thank you so much.
[Data],,,,,,, SampleName,SamplePlate,SampleGroup,PoolID,Project,SampleWell,SentrixID,Sentrix_Position HCT8-0h-1,,S,,,,GSM2140588,R01C01 HCT8-0h-2,,S,,,,GSM2140589,R02C01 HCT8-0h-3,,S,,,,GSM2140590,R03C01 HCT8-5Fu-0h-1,,R,,,,GSM2140594,R01C02 HCT8-5Fu-0h-2,,R,,,,GSM2140595,R02C02 HCT8-5Fu-0h-3,,R,,,,GSM2140596,R03C02 HCT8-5Fu-72h-1,,R,,,,GSM2140597,R04C02 HCT8-5Fu-72h-2,,R,,,,GSM2140598,R05C02 HCT8-5Fu-72h-3,,R,,,,GSM2140599,R06C02