GenomicRatioSet object after minfi normalization does not show method used for preprocessing.

Question

[samuel.carleial]

Hi all,

(I did not find a similar issue in other posts)

Using R to preprocess my raw methylation data (Illumina EPIC Beadchip), I wanted to compare the different preprocessing methods in minfi. So, I ran for the same rgset object the following functions:

1. preprocessSWAN()
2. preprocessFunnorm()
3. preprocessNoob()
4. preprocessQuantile()

When I access the metadata, by simply calling the name of the preprocessed rgsets, I get a summary of the object, for example:

rgset_qcsampleprobe_norm_funn
> class: GenomicRatioSet 
> dim: 847058 365 
> metadata(0):
> assays(2): Beta CN
> rownames(847058): cg14817997 cg26928153 ... cg07587934 cg16855331
> rowData names(0):
> colnames(365): 205045550101_R01C01 205045550101_R02C01 ...
>   205045550074_R02C01 205045550074_R03C01
> colData names(30): sample_id sample_name ... yMed predictedSex
> Annotation
>   array: IlluminaHumanMethylationEPIC
>   annotation: ilm10b4.hg19
> Preprocessing
>   Method: NA
>   minfi version: NA
>   Manifest version: NA

Is it a bug (EPIC not 450k?) or why does the metadata from this object does not show the preprocessing information?

Thanks