search

hansenlab / minfi

Devel repository for minfi
58 stars 68 forks source link

mapToGenome for the EPIC data #102

Closed hcli0325 closed 7 years ago

hcli0325 commented 7 years ago

Hi! I am using the mapToGenome function to get genome annotation for my Illumina HumanMethylation EPIC data. Here is my code: myDataGenome<-mapToGenome(myDataSIBoth) and here is the returned message: Loading required package: IlluminaHumanMethylationEPICanno.ilmn10.hg19 Error in getAnnotationObject(object) : cannot load annotation package IlluminaHumanMethylationEPICanno.ilmn10.hg19 It seems to me that the " IlluminaHumanMethylationEPICanno.ilmn10.hg19" package has been updated to “ IlluminaHumanMethylationEPICanno.ilmn10b2.hg19”. So I guess maybe the released version of minfi did not include this update? Thanks.

kasperdanielhansen commented 7 years ago

When you create your data objects in minfi they link to "current" annotations. In this case "IlluminaHumanMethylationEPICanno.ilmn10.hg19" has (was) declared unsupported by Illumina, so we do not release this anymore. The best thing is probably to recreate your objects using read.meth.exp(). It is possible to do shortcuts by modifying the annotation slot, but that is for experts.

kasperdanielhansen commented 7 years ago

So in case I was not clear: you created your object using an old version of minfi and you're analyzing it using a newer version.