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🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
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Grn IDAT does not exist #124

Open mel-14 opened 12 months ago

mel-14 commented 12 months ago

Hello, I have just started using the sesame package to work on my normalization for methylation data and have run into troubles with defining and IDAT directory and the subsequent openSesame step.

My configuration R: 4.3.1 BiocManager: 1.30.22 Sesame: 1.20.0 sesameData: 1.30.22 ExperimentHub: 2.10.0

I used the code

Library(sesame) IDAT_dir <- system.file(“/path/to/directory/”, package = “sesameData”) betas = openSesame(IDAT_dir, BPPARAM = BiocParallel::MulticoreParam(2))

Which results in the following error message; Error in readIDATpair(x, platform = platform, manifest = manifest) : Grn IDAT does not exist

Looking into the idat_dir path yields:

IDAT_dir [1] ""

There appears to be another person with a similar issue from 3 weeks ago. Issue is still standing.

Thank you

zwdzwd commented 11 months ago

Please use 

IDAT_dir <- “/path/to/directory/”
betas = openSesame(IDAT_dir, BPPARAM = BiocParallel::MulticoreParam(2))

The system.file is for retrieving an example when it's unavailable. Sorry for confusion. I will clarify this in the vignette