Findind the annotation file of the Illumina Infinium HumanMethylation450k array

Question

[Chris K]

Hello to everyone,

Sorry if this is a trivial question, but it is my first time working on array data analysis (I was more into the bioinformatics engineering). I am trying to recreate the results of a papper, for training purposes that conducted an experiment with Illumina Infinium HumanMethylation450k array. Before going into the coding, at the part of the files that were used it states that will need the idat files, the Sample sheet and the annotation file of the Illumina Infinium HumanMethylation450k. My question is where i can find this file.

Thank you all in advance!

P.S:

I did some searching by myself, and landing on this https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html and i guess the correct file is the "HumanMethylation450 v1.2 Manifest File" but i am asking in order to either verify that this is it or find that it is a completely different file.

[GenoMax]

You can also find the files here: https://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit/downloads.html

Be sure to check the version of the array data you have and use the appropriate files.

Answer 1

[yura.grabovska]

Hi, what paper are you trying to recreate?

One of the most common approaches to analysis methylation array data is to use R packages like minfi. It has a bunch of functions for working with preprocessing, normalisation and annotation of IDAT files from Illumina.

Here's some code for R

library(minfi)

idat.dir <- "/path/to/idat/files/"

## idat files come in pairs, but you need to feed minfi just the basename
bnames <- gsub("_Red.idat", "", list.files(idat.dir, pattern = "_Red.idat", full.names = TRUE))

## read in the idats
RGset <- read.metharray(basenames = bnames, force = TRUE)

# normalise with single-sample NOOB
Mset <- preprocessNoob(RGset)

## ratio convert to beta-values
beta.values <- getBeta(Mset)

library(DMRcate)

## remove poorly performing probes
filt.beta.values<- rmSNPandCH(beta.values)

## get the array annotation for the 450k object, also works with EPIC
array.anno <- getAnnotation(Mset, lociNames = rownames(filt.beta.values))

[Chris K]

The actual papper is a Master thesis of an acquaintancethat has not been published yet, just now he sent me the whole R script. And in a part he did not include, he had a version of the code similar to what you provided. Thank you very much for your quick response!

[yura.grabovska]

Let me know if you have any further questions. A big chunk of my dayjob includes working with methylation arrays so happy to help