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hansenlab / minfi

Devel repository for minfi
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After running quantile normalization, the new GMset still shows "Raw" in preprocessing method #128

Open zhaozhongzhu opened 6 years ago

zhaozhongzhu commented 6 years ago

Hi Dr Hansen When I ran this preprocessQuantile function, it seems it was sucessful. However, when I take a look at the GMset, the method part of Preprocessing still shows "Raw (no normalization or bg correction)". Do you know why this happens?

Another question is after the normalization, I want to extract beta values to do association test, like linear regression. But the format of GMset is minfi, is there a way to only get the beta values out with column and row names as sample and cpg?

Thank you very much!

ZZ

GMset <- preprocessQuantile(RGset1,fixOutliers = TRUE,quantileNormalize = TRUE,stratified = TRUE,mergeManifest = FALSE,sex = NULL,verbose = TRUE) [preprocessQuantile] Mapping to genome. [preprocessQuantile] Fixing outliers. [preprocessQuantile] Quantile normalizing.

GMset class: GenomicRatioSet dim: 855184 16 metadata(0): assays(2): M CN rownames(855184): cg14817997 cg26928153 ... cg07587934 cg16855331 rowData names(0): colnames(16): 200325570151_R01C01 200325570151_R02C01 ... 200325570152_R03C01 200325570152_R04C01 colData names(14): Sample_Name Sample_Well ... filenames predictedSex Annotation array: IlluminaHumanMethylationEPIC annotation: ilm10b2.hg19 Preprocessing Method: Raw (no normalization or bg correction) minfi version: 1.20.2 Manifest version: 0.3.0