chiaraherzog/illuminamousemethylationmanifest

This package provides Illumina Mouse Methylation Array Manifest (12.v1, Genome Build mm10) compatible with minfi.

illuminamousemethylationmanifest's Issues

Issues preprocessing the data in minfi

Hello,
I am currently trying to analyze IDAT files from the mouse methylation array but I am having trouble to preprocess the data.
The preprocessFunnorm and the preprocessQuantile functions from the minfi package don't work.

preprocessFunnorm(RGset) gives the error : Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent

preprocessQuantile(RGset) gives the error : Error in normalize.quantiles(mat[Index2, ]) : Matrix expected in normalize.quantiles

On the otherhand

preprocessNoob seems to works, outputting a MethylSet object, while still giving this : Warning: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.Warning: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.

Has anyone encountered this issue ?
Has the minfi package combined with these mouse packages work for others ?
I already analyzed my data using the sesame package which supported the mouse array but I now want to integrate my methylation data with expression data and I would like to use the MEAL package but it only supports methylation data preprocessed with minfi.
Hope someone will read this,
Thank you,
NVD

Thanks for doing this. Getting an error with minifi::mapToGenome

Following the minifi instructions, then applying as per the README:

RGset@annotation <- c(array = "IlluminaMouseMethylation", annotation = "12.v1.mm10")

yields an error when using mapToGenome:

GRset <- mapToGenome(RSet)

Loading required package: IlluminaMouseMethylationanno.12.v1.mm10 Error in getAnnotationObject(object) : cannot load annotation package IlluminaMouseMethylationanno.12.v1.mm10 In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘IlluminaMouseMethylationanno.12.v1.mm10’