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hansenlab / minfi

Devel repository for minfi
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Error in creating RGSet using read.metharray.exp function in R #211

Closed kendrix10 closed 3 months ago

kendrix10 commented 4 years ago

I am working with Illumina 450K DNA methylation data using the minfi package in R. I am trying to creating an RGSet object from idat files and encountered this error: "Error in xx[commonAddresses, "Mean"] : subscript out of bounds".

path = "~/kendrix/macular_degeneration/data/idats/E-MTAB-5535"
targets <- read.metharray.sheet(path)
baseDir <- system.file(path, package = "minfiData")
sub(baseDir, "", targets$Basename)

#Create RGSet object.
AE_RGSet <- read.metharray.exp(targets = targets, verbose = TRUE)

I've been using the read.metharray.exp function to create RGSet objects multiple times before for other projects, but this is the first time I've encountered this problem. I tried to use the same function to create RGSet object for another project and it works, so I'm not sure why this error occurred.

I've checked my idat files against my samplesheet, which was necessary to create the RGSet object, and all the idats match the samples in the samplesheet.

I'm using R version 3.6.3 and minfi version 1.32.0. Any help or suggestions are appreciated. Thank you.