Hello

I'm currently working with methylation data from a number of studies (all 450k arrays). I have IDAT files for most, although a few only supply methylated/unmethylated signals on GEO. I have contacted authors and the IDAT files are unrecoverable. My question is whether or not it is possible to carry out any preprocessing or normalisation on the meth/unmeth.txt signals on GEO? 

I have converted the meth/unmeth.txt signals to a GenomicMethylSet with readGEORawFile from which I can remove X/Y chromosomes, cross-reactive probes etc. What I can't seem to do is identify a method of being able to obtain p values for the probe reads or carry out any normalisation. The original meth/unmeth.txt signals have a detection Pval column for each sample and probe, although it is mainly occupied by 0's with the occasional 1 eg;

REF_ID      Samp1.Signal_A     Samp1.Signal_B    DetectionPVal

cgXXX              1000                           2000                        0

cgXXX              1000                           2000                        0

cgXXX              1000                           2000                        1

Any suggestions on how to get around this would be greatly appreciated. Alternatively, if it is not possible with the data supplied on GEO that would also be good to confirm so I can discard the studies from the analysis.

Thank you in advance.