Start with methlyation level table

[albert-ying]

Hi, thank you for the amazing tool! I found that all of the tutorial requires to start with .idat file. However, some GEO dataset doesn't provide the original .idat file. For example, the Hannum dataset GSE142536, which only provides the methylation ratio at each CpG site in each sample.

I'm wondering if it is possible to start with such kind of table (i.e. skip the QC step) and apply the rest of the normalization procedures to such kind of data?

Thank you!

[perishky]

Unfortunately, this isn't possible currently. Adapting the normalization procedure would be fairly straight-forward if the raw data files available on GEO provided all probe intensities. They do typically include columns providing the methylated and unmethylated probe intensities for most probes. Unfortunately, control probe intensities are typically missing (this includes the Hannum dataset). Given that functional normalization is based on removing control probe variation from probe intensity quantiles, it's unclear to me how functional normalization can be applied meaningfully when the control probes are not available.

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________________________________ From: albert-ying ***@***.***> Sent: 31 December 2021 10:34 AM To: perishky/meffil ***@***.***> Cc: Subscribed ***@***.***> Subject: [perishky/meffil] Start with methlyation level table (Issue #36) Hi, thank you for the amazing tool! I found that all of the tutorial requires to start with .idat file. However, some GEO dataset doesn't provide the original .idat file. For example, the Hannum dataset GSE142536, which only provides the methylation ratio at each CpG site in each sample. I'm wondering if it is possible to start with such kind of table (i.e. skip the QC step) and apply the rest of the normalization procedures to such kind of data? Thank you! — Reply to this email directly, view it on GitHub<#36>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACSRUULBBTTCOIAWXXOUKETUTWBMXANCNFSM5LBDUCRA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[albert-ying]

Yeah that makes sense... At least the impute cell type function supports the beta matrix, which is all I need for now. Thank you so much!

[epzjlm]

You can also generate a normalization report from the beta matrix if of interest:[https://github.com/perishky/meffil/wiki/Generate-normalization-report-from-normalised-betas]