EPIC v2 preprocessQuantile()

[psychesha21]

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!