SeSAMe DMR for EPIC V2
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luca.s ▴ 50
@lucas-24386
Last seen 14 days ago
Italy

Hi, we are analyzing EPIC V2 arrays with SeSAMe v.1.23.2. When we follow the github tutorial and try and identify DMR, with the DMR function specifying platform="EPICv2", the following error pops up: Merging correlated CpGs ... Error in seq_len(n.cpg - 1) : argument must be coercible to non-negative integer Error during wrapup: 'length = 4' in coercion to 'logical(1)'

No error if we specify "EPIC" as platform. Does anyone have a hint on how to solve this? At the bottom you find the versions for the different packages used. Thanks

R: 4.4.0 Bioconductor: 3.20 sesame: 1.23.2 sesameData: 1.23.0 ExperimentHub: 2.13.0

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
sesame EPICv2manifest epicv2 • 250 views
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zhouwanding ▴ 20
@zhouwanding-15106
Last seen 22 days ago
United States

My guess is that the input has a suffix-removed probe id for EPICv2 data. We will add a fix to that in the DMR function in a few days. But can you verify this is the case?

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Update: The new 1.23.8 should have fixed this issue. Let me know if it still doesn't.

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Thank you, that was indeed the case. I fed the function with the data containing the replicate probes collapsed by mean and this caused the error.

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