I'm Adam and I'd like to analyze data from methylation microarrays by Illumina. As far as I know there is specific software (GenomeStudio) which allows to preprocessing raw microarray data, then it can be processed in R by lumi package. Nevertheless I'd like to avoid GenomeStudio preprocessing step and analyze my data only with packages implemented in bioconductor.
The analyze pf Affymetrix datasets (.CEL files) doesn't seem to be quite difficult (may tutorials and lenghty manuals).
In case of illumina there are of course good manuals but only for files firstly preprocessed by GenomeStudio.
Files loaded by lumi(from GenomeStudio) and illuminaio(totally raw data) are visibly different.
So my question is what packages and functions should I use to analyze my data to do normalization, quality control, filtering, testing, clustering and finally visualization and interpretation:
data <- readIDAT(my_data)
Of course I don't look for some step by step tutorials or complete solutions, but I'll be very grateful for some hints and tips or show me where shoild I look.