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De seq2 formula

Philippe BORDRON requested to merge DESeq2-formula into master

Description

An hidden way that allow to ignore factors or/and plate effect if needed. User must know what he does when using it. This is a proposal, so fell free to comment this PR (ping @eric.charpentier)

How to use it

In order to ignore factor or plate effect, user must add a "normalizationOptions" entry in the comparisons part of the project in the config.json. The entry must describes a list that contains "--ignore-plate-effect" or/and "--ignore-batch-effect".

Example:

{
    ...
    "comparisons": {
        "TestProject": {
            ...
            "normalizationOptions" : ["--ignore-plate-effect"],
            ...
        }
    }
}

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