I'm trying to analyze methylation data from the Illumina Infinium Mouse Methylation Array. I opted for SeSAMe since it seems to have built-in support for exactly this array. However, it seems that the platform is somehow ambigous. Some functions fail with the following error message: "Error in inferPlatformFromProbeIDs(sdf$Probe_ID, silent = !verbose) : Ambiguous platform. Please provide platform explicitly."
I generated sigDFs with
sdfs = openSesame(idat_dir, func = NULL)
and when I run for example
inferSpecies(sdfs, return.species = TRUE)
I get the mentioned error message. I tried to "provide platform explicitly" by generating the sigDFs with
sdfs = openSesame(idat_dir, func = NULL, platform = "MM285")
but with the same result.
I also tried to provid the species explicitly by
sdfsm = updateSigDF(sdfs, species="mus_musculus")
but that didn't help either. I should mention that I haven't tampered with the IDAT files in any way, and they were delivered by the quite trustworthy governmentally funded SciLifeLab, so I expect them to be correct. Furthermore, I've been able to run some analysis with minfi, so they really seem to be OK.