Entering edit mode
Hi, has anyone worked with data from the new Illumina Epic dataset? It has over 850K vs 450K. I tried using methyAnalysis but getting errors because there does not seem to be any annotation packages like the IlluminaHumanMethylation450k.db.
This is my first time doing methylation analysis; so I'm stuck. Does anyone know what other packages/technique I can use to get around this annotation problem? I do not have the IDAT files but outputs from genomestudio as provided by our vendor. I could possibly get the IDAT files though if it helps.
Thank you in advance.
Ahdee
Peter, this is awesome. Stupid question but I see two files, one is a manifest file? Do I just download and install this as usual with install.packages function? Thanks.
Would I also be able to use this with other packages like lumi: for example lumiMethyR requires an annotation IlluminaHumanMethylation450k.db, can I do something like, lumiMethyR("input.txt",lib="IlluminaHumanMethylationEPICanno.ilmn10.hg19") instead? thanks.
I don't know off hand whether it works out-of-the-box with lumi. Perhaps give it a try and report back with how you go.
I followed your posts and tried to load it in lumi, and got the error:
rawdata <- lumiMethyR("MethylationProfile.txt",lib="IlluminaHumanMethylationEPICanno.ilm10b2.hg19")
Error in match(x, table, nomatch = 0L) : object 'allAnnotation' not found
I am extremely new to the analysis. Any idea? Thank you.
double post