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hansenlab / minfi

Devel repository for minfi
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EPIC v2 preprocessQuantile() #274

Open psychesha21 opened 6 months ago

psychesha21 commented 6 months ago

Hi,

I'm using quantile normalization for my Red green channel set from EPICv2 data. I didn't see any errors, but the output of the preprocessQuantile() returns "Method: Raw (no normalization or bg correction)". So did it normalized my data correctly or not? Here are my code and output:

rg123 class: RGChannelSet dim: 1105209 123 metadata(0): assays(2): Green Red rownames(1105209): 1600157 1600179 ... 99810982 99810990 rowData names(0): colnames(123): 207096540008_R04C01 207096540008_R05C01 ... 207097650076_R04C01 207097650076_R05C01 colData names(9): Sample_Name Sample_Well ... Basename filenames Annotation array: IlluminaHumanMethylationEPICv2 annotation: 20a1.hg38 GRset.quantile <- preprocessQuantile(rg123, fixOutliers = TRUE,

  • removeBadSamples = TRUE, badSampleCutoff = 10.5,
  • quantileNormalize = TRUE, stratified = TRUE,
  • mergeManifest = FALSE, sex = NULL) [preprocessQuantile] Mapping to genome. [preprocessQuantile] Fixing outliers. [preprocessQuantile] Quantile normalizing. GRset.quantile #dim: 930075 123 class: GenomicRatioSet dim: 930075 123 metadata(0): assays(2): M CN rownames(930075): cg00381604_BC11 cg21870274_BC21 ... cg27912920_TC21 cg16855331_BC21 rowData names(0): colnames(123): 207096540008_R04C01 207096540008_R05C01 ... 207097650076_R04C01 207097650076_R05C01 colData names(12): Sample_Name Sample_Well ... yMed predictedSex Annotation array: IlluminaHumanMethylationEPICv2 annotation: 20a1.hg38 Preprocessing Method: Raw (no normalization or bg correction) minfi version: 1.51.0 Manifest version: 1.0.0

Thanks for your attention!