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cgplab / Rockermeth

A tool for discovering Differentially Methylated Regions
MIT License
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Inquiry Regarding Your Study in "Charting differentially methylated regions in cancer with Rocker-meth" #9

Open BioDataMiner opened 5 months ago

BioDataMiner commented 5 months ago

I recently read your article titled "Charting differentially methylated regions in cancer with Rocker-meth" published in Communication Biology, and I found your research both intriguing and highly informative. I am writing to seek clarification regarding the supplementary data provided in your paper. Specifically, I have questions about Supplementary Data 6 and its relationship to Supplementary Data 5.

1) Is Supplementary Data 6 the result of processing the table in Supplementary Data 5? If not, could you please explain how Supplementary Data 6 was obtained? 2) According to the article, the filtering criteria included a mean beta difference >5. However, I noticed that Supplementary Data 6 contains some DMRs with a mean beta difference <5, such as chr1:977895-991567. Could you clarify why these DMRs are included? 3) Additionally, I observed that some DMRs listed for certain cancer types in Supplementary Data 6, such as HNSC_hypoway chr1:809468-834295, do not appear in Supplementary Data 5. Could you explain the reason for these discrepancies?

romagnolid commented 5 months ago

Hello, thanks for you comment, I'll give it a look ASAP