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Question: Subsetting samples and columns of a MethyLumiSet subsets QC probes
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gravatar for alan.ocallaghan
19 days ago by
alan.ocallaghan10 wrote:

Loading 450k methylation data as follows: methyset <- methylumIDAT(barcodes=barcodes, parallel=TRUE, idatPath="./data/IDATS")

Then the following code will error (subscript out of bounds): methyset[1:1000, 1:2]

This is because there are only 850 QC probes, which should not be subset with the indices used on the main dataset.

The code responsible is below: https://github.com/Bioconductor-mirror/methylumi/blob/master/R/MethyLumiSet-class.R#L454

ADD COMMENTlink modified 19 days ago by Sean Davis21k • written 19 days ago by alan.ocallaghan10
0
gravatar for Sean Davis
19 days ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Thanks for the report. This should be fixed in 2.24.1 (release) and 2.25.1 (devel) versions.

ADD COMMENTlink written 19 days ago by Sean Davis21k
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