I have RGset generated from idat files, these idats are produced from EPIC V2 arrays. After generating the RGset, by code: RGSet@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38"), I generated the Mset successfully by the code: preprocessRaw(RGSet)
I have problems during normalization with the following functions:
1- preprocessFunnorm: (GRset_funnorm <- preprocessFunnorm(RGSet, bgCorr = TRUE, dyeCorr = TRUE, keepCN = TRUE, ratioConvert =TRUE,verbose = TRUE), I got this error:
[preprocessFunnorm] Background and dye bias correction with noob Error in if (s == 0) stop("cannot estimate scale: MAD is zero for this sample") : missing value where TRUE/FALSE needed.
2- MSet_norm <- preprocessQuantile(RGSet), I got this error:
[preprocessQuantile] Mapping to genome.
Error in kmeans(dd, centers = c(min(dd), max(dd))) :
initial centers are not distinct
3- > preprocessNoob(RGSet)
Error in if (s == 0) stop("cannot estimate scale: MAD is zero for this sample") :
missing value where TRUE/FALSE needed
although I removed all bad quality at thershold 10.5, would anyone help with this error please??
I have RGset generated from idat files, these idats are produced from EPIC V2 arrays. After generating the RGset, by code: RGSet@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38"), I generated the Mset successfully by the code: preprocessRaw(RGSet)
I have problems during normalization with the following functions:
1- preprocessFunnorm: (GRset_funnorm <- preprocessFunnorm(RGSet, bgCorr = TRUE, dyeCorr = TRUE, keepCN = TRUE, ratioConvert =TRUE,verbose = TRUE), I got this error:
[preprocessFunnorm] Background and dye bias correction with noob Error in if (s == 0) stop("cannot estimate scale: MAD is zero for this sample") : missing value where TRUE/FALSE needed.
2- MSet_norm <- preprocessQuantile(RGSet), I got this error:
[preprocessQuantile] Mapping to genome.
Error in kmeans(dd, centers = c(min(dd), max(dd))) :
initial centers are not distinct
3- > preprocessNoob(RGSet)
Error in if (s == 0) stop("cannot estimate scale: MAD is zero for this sample") :
missing value where TRUE/FALSE needed
although I removed all bad quality at thershold 10.5, would anyone help with this error please??