Hi, I tried to read an idat file with R package illuminaio:
library(illuminaio)
idatfile <- 'C:/Users/Tania/Documents/GSE26677/GSE26677_non-normalized.txt'
idat <- readIDAT(idatfile, what='all')
and also with limma package:
library(limma)
bigxfile <- 'C:/Users/Tania/Documents/GSE26677/FILE/GPL6884_HumanWG-6_V3_0_R0_11282955_A.bgx'
idat <- read.idat(idatfile, bigxfile)
and got this error:
Error in readIDAT(idatfile, what = "all") :
Cannot read IDAT file. File format error. Unknown magic: ID_R
Seems something is wrong with idat file, but I tried these commands with several different idat files on GEO (GSE22247, GSE79308, GSE43336, GSE26677) and always got that error.
Does anyone know how to solve this?
The top of idat file is:
ID_REF NSP Detection Pval SP Detection Pval
ILMN_1762337 75.85098 0.2555995 68.39282 0.6166008
ILMN_2055271 92.8892 0.03820817 95.76293 0.02371541