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FoxoTech / methylcheck

Python-based Illumina methylation array quality control software.
MIT License
10 stars 6 forks source link

SVA and ComBat #4

Open brianchengithub opened 6 years ago

brianchengithub commented 6 years ago

To control for batch-effects, we need the 'sva' and 'ComBat' commands from the 'sva' Bioconductor package: https://bioconductor.org/packages/release/bioc/html/sva.html

marcmaxson commented 5 years ago

ComBat -- controls for batch-specific variation, based on the bioconductor package. Requires a separate file, called QC summary/report, contains QC1, PG, etc and batch scores. minfi deals with file format variance with a user "merge" function to tidy it up.

SVA - surrogate variable analysis, like PCA, to capture latent batchness variable. Assumes largest signal is the batch signal, but may be invalid assumption. (more recent approach)

marcmaxson commented 5 years ago

Randy: towards a namespace of data objects from labs, not a zipfile of different arbitrary files. methQC should mimic the skilearn style interface.

1 - create objects of algos 2 - each has logical functions (init, fit, transform, etc) within that object. same names across functions