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Error during normalization using different minfi functions #279

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ralanany opened this issue Sep 2, 2024 · 0 comments
Open

Error during normalization using different minfi functions #279

ralanany opened this issue Sep 2, 2024 · 0 comments

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@ralanany
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ralanany commented Sep 2, 2024

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??

@ralanany ralanany changed the title I have RGset generated from idat files, these idats are produced from EPIC V2 arrays, After generating the RGset, RGSet_14@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38") I have RGset generated from idat files, these idats are produced from EPIC V2 arrays, After generating the RGset, RGSet_14@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38"), Then I generated the Mset successfully. The problem is during normalization by preprocessFunnorm, using this code (GRset_14_funnorm <- preprocessFunnorm(RGSet_14_keep, 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. although I removed all bad quality at thershold 10.5, would anyone help with this error please? Sep 2, 2024
@ralanany ralanany changed the title I have RGset generated from idat files, these idats are produced from EPIC V2 arrays, After generating the RGset, RGSet_14@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38"), Then I generated the Mset successfully. The problem is during normalization by preprocessFunnorm, using this code (GRset_14_funnorm <- preprocessFunnorm(RGSet_14_keep, 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. 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, using code: RGSet@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38"), Then I generated the Mset successfully. The problem is during normalization by preprocessFunnorm, using this code (GRset_14_funnorm <- preprocessFunnorm(RGSet_14_keep, 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. although I removed all bad quality at thershold 10.5, would anyone help with this error please? Sep 2, 2024
@ralanany ralanany changed the title I have RGset generated from idat files, these idats are produced from EPIC V2 arrays, After generating the RGset, using code: RGSet@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38"), Then I generated the Mset successfully. The problem is during normalization by preprocessFunnorm, using this code (GRset_14_funnorm <- preprocessFunnorm(RGSet_14_keep, 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. 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, using code: RGSet@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38"), Then I generated the Mset successfully. The problem is during normalization by preprocessFunnorm, using this code (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. although I removed all bad quality at thershold 10.5, would anyone help with this error please? Sep 2, 2024
@ralanany ralanany changed the title I have RGset generated from idat files, these idats are produced from EPIC V2 arrays, After generating the RGset, using code: RGSet@annotation <- c(array = "IlluminaHumanMethylationEPICv2", annotation = "20a1.hg38"), Then I generated the Mset successfully. The problem is during normalization by preprocessFunnorm, using this code (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. although I removed all bad quality at thershold 10.5, would anyone help with this error please? Error during normalization using different minfi functions Sep 2, 2024
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