QC: Use detection p-values for probes to determine sample and probe failures

FoxoTech / methylcheck

Python-based Illumina methylation array quality control software.

MIT License

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QC: Use detection p-values for probes to determine sample and probe failures #6

Closed brianchengithub closed 3 years ago

brianchengithub commented 5 years ago

[x] Compute detection p-values for each probe.
[x] User-defined threshold for 'probe failure' (detection p > 0.05)
[ ] Samples with <90% of high-confidence probes should be removed from further analysis
[x] Export separate CSV files for sample failures and probe failures.

marcmaxson commented 5 years ago

note: this is part of minfi and sesame already. to be useful, needs to support more flexibility. same probe doesn't fail on all samples at once, so support that.

marcmaxson commented 3 years ago

updating this. Maybe explain more about this one?

Samples with <90% of high-confidence probes should be removed from further analysis

And for this, do you want a separate pickled file of all the failed data? Options only allow it to return the passing data. @brianchengithub

brianchengithub commented 3 years ago

@marcmaxson Disregard that remaining item. Since 10/24/2018 we've discussed no probe exclusion, and providing recommended exclusions to the users at the end.