So I used the IlluminaHumanMethylation450k.db annotation package to find the probes associated with particular genes of interest. I sent my code to a colleague, but she received the following warning when loading the annotation package.
3: 'IlluminaHumanMethylation450k.db' is deprecated. Use 'FDb.InfiniumMethylation.hg19' instead. Use 'FDb.InfiniumMethylation.hg18' instead. Use 'mapToGenome() function in minfi or methylumi' instead.
The 'FDb.InfiniumMethylation.hg19' package doesn't seem to have the gene names associated to each probe, so my question is, can we use the gene-to-probe mapping found in 'IlluminaHumanMethylation450k.db' for the 'FDb.InfiniumMethylation.hg19' annotation?