Annotation in minfi

by Jean-Philippe Fortin

With the release of Bioconductor 2.13 comes a new release of minfi, a powerful tool for the analysis of methylation data from Illumina 450k arrays.  Some of you may have noticed that in Bioconductor 2.13, the annotation package IlluminaHumanMethylation450kanno.ilmn.v1.2, required by the previous versions of minfi, does not exist anymore.  What’s happening. Well, a new annotation package took its place, and is called IlluminaHumanMethylation450kanno.ilmn12.hg19. But when one tries to manipulate previously created RGChannelSet‘s with the new version of minfi, the following error is thrown:

“there is no package called ‘IlluminaHumanMethylation450k.anno.ilmn.v1.2”

That’s because you need to update your annotation. But don’t worry, minfi’s authors have thought about it; here is how to quickly fix it:

yourRGSet <- updateObject(yourRGSet)

and your RGSet will now have the right annotation. Simple. In particular, shinyMethyl could not load on a new BioC session because of the non-existence of the old annotation package. Now it’s fixed, and users are invited to reinstall the package from gitHub.