minfi error in read.metharray
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researcher • 0
@researcher-20723
Last seen 21 months ago

I am getting following error related to read.metharray, while running my Script,

Error in read.metharray(basenames = files, extended = extended, verbose = verbose,  : 
  !anyDuplicated(basenames) is not TRUE

FYI, I made my sample sheet on my own by removing the information of some of the samples for which the data was missing. I have double checked that now my meth_idat folder has exactly the same number of samples each with 2 idat files as mentioned in my sample sheet. But still getting this error.

Any help will be highly appreciated.

Thanks

minfi methylation idat samplesheet • 1.1k views
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@kasper-daniel-hansen-2979
Last seen 10 weeks ago
United States

If you're using read.metharray, the base names argument is a vector which is half the length of the number of files, equal to the number of samples. You need to remove the _Grn and _Red from the file names and remove any duplicates.

read.metharray.exp() is probably an easier to use interface.

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Hi there, I'm completely new to methylation analysis so apologies for my naivety! I have used the EPIC beadchip (8 sample) for my experiment. I'm also having this issue when I try to read the data into R. The idat files are named like this:

205128000104_R01C01_Grn.idat

205128000104_R01C01_Red.idat

From the above post do you mean I need manually edit the idat file names for it to be recognised? Because doing so would overwrite one of the files. Or have I misunderstood? I have attached a picture of my sample sheet.

Any help would be greatly appreciated.enter image description here

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