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gustaveroussy / EaCoN

Easy Copy Number !
MIT License
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Change the reference for Affymetrix arrays #17

Closed jgarces02 closed 3 years ago

jgarces02 commented 5 years ago

Hi (again) @CS-GustaveRoussy,

I guess the currently approach of EaCoN is taking account those references provided by Affymetrix to determine CNVs, am I right? Would be another way to build and use a custom reference, eg. compare normal-tumor CELs? (I know that rawcopy is able to do this with rawcopy.makeReference, but it's difficult to understand because it's poorly documented).

Thanks a lot!

aoumess commented 3 years ago

Sorry for not answering your question (years) before ! I understand your request but this is something that appends above EaCoN's process, namely in APT (Affymetrix Power Tools). I think you can build your own reference dataset, though this seems to be quite complicated. I probably won't write an official support to handle non-standard (ie, those provided with EaCoN dependencies, initially provided by Affymetrix) reference packages, simply as it would slightly over-complicate the use of EaCoN for only a single feature request yet. If other people ask for it, then I'll go for it.

Cheers