I would like to perform methylation data analysis and have data from both 450K and EPIC. I created a csv file containing the sentrix ID, sentrix position and basename which contains path to the IDAT files which are all in the same folder (including the csv).
library(methylationArrayAnalysis) library(knitr) library(limma) library(minfi) library(IlluminaHumanMethylation450kanno.ilmn12.hg19) library(IlluminaHumanMethylation450kmanifest) library(RColorBrewer) library(missMethyl) library(minfiData) library(Gviz) library(DMRcate) library(stringr) library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) library(conumee)
dataDirectory <- "C:/Users/35389/Desktop/Medullos/All_combined" target <- read.metharray.sheet(dataDirectory, pattern = "sample_sheet_2.csv") target target$Basename g_files <- paste0(target$Basename, "_Grn.idat") all(file.exists(g_files))
# read in the sample sheet for the experiment rgset <- read.metharray.exp(targets = target, recursive = TRUE, verbose = TRUE, extended = TRUE)
However, when I read in the files using read.metharray.exp() I get the following error
Timing stopped at: 0.14 0.05 0.22 Error in readIDAT(xx) : Cannot read IDAT file. File format error. Unknown magic:
Any help will be greatly appreciated! Thanks in advance :)