I am trying to read Illumina Human WG6v2 microarray raw IDAT files using the read.idat command implemented in the limma package. However, I encounter an error which seems to come from the BGX manifest file. When I indicate the correct BGX file, I obtain a read.idat error, as seen below in the code example (highlighted text). Could this be due to an incorrect BGX file? I obtained it directly from Illumina... Why else would the parser give this error?
Inter alia, I am able to read individual IDAT files using the readIDAT command in the illuminaio package. But I cannot seem to combine many IDAT files into an EList-raw class object...
> library(limma) > IDATfiles <- list.files(pattern ="\\.idat") > read.idat(IDATfiles, bgxfile = "HumanWG-6_V2_0_R2_11223189_A.bgx") Reading manifest file HumanWG-6_V2_0_R2_11223189_A.bgx ... Done 4062786004_A_Grn.idat ... Done Error in read.idat(IDATfiles, bgxfile = "HumanWG-6_V2_0_R2_11223189_A.bgx") : Can't match ids in manifest with those in idat file4062786004_A_Grn.idat- please check that you have the right files > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite) locale:  en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages:  stats graphics  grDevices utils  datasets methods  base other attached packages:  limma_3.24.10 loaded via a namespace (and not attached):  base64_1.1  illuminaio_0.10.0