Hello,

I am currently trying to use the MethylAid package to visualize methylation array data in the form of idat files. My directory of files contains the idat, jpg, locs and xml files. I am trying to follow the tutorial from https://www.bioconductor.org/packages/release/bioc/vignettes/MethylAid/inst/doc/MethylAid.pdf but am having trouble understanding some of the variables. First I load my idat files with 

idatFile <- list.files(pattern = "idat", full.name = TRUE)

but when I try the next line

targets <- read.table(idatFile, header = TRUE, sep = "\t")

it gives me an error: Error in file(file, "rt") : invalid 'description' argument

From what I understand, this error is because idatFile is not a single item. I am open to suggestions.

Thanks,

Julian

Hi Julian,

To use MethylAid you first have to create a targets file e.g. "targets.csv". This file contains the sample description, for example, a column with Sample_Names, the Sample_Wells and Sample_Plates etc. Usually, such a file is also provided by the data generation centre. You should add a column called  'Basename'  which, for each sample, contains the path to the idat-files. In your case this will be something like:

Basename <- gsub("_Red.idat|_Grn.idat", "", idatFile).

MethylAid uses the idat-reading functionality from the minfi-package. For more details on creating a targets-file see the vignette of minfi:

http://bioconductor.org/packages/release/bioc/vignettes/minfi/inst/doc/minfi.pdf

If you have any further questions about MethylAid let me known!

Cheers,

Maarten