INNER CODE UNIT · Python

P

antigenomics/vdjtools · python/vdjtools/cli/__init__.py:369

                P = 2*P_avg / (1 + exp(-Z)).  Corrects a batch that is merely
                NOISIER in a gene, which the location adjustment cannot.

    NAME THE TECHNICAL VARIABLE. Point --batches at a primer mix, a run, an extraction protocol.
    Pointing it at a study identifier that is collinear with the biology being measured removes
    the effect along with the batch, and nothing reports that it happened.
    """
    from vdjtools import preprocess
    from vdjtools.io.batch import read

    if len(samples) < 2:
        _err("correct-vj needs at least two samples — a batch effect is a between-batch quantity")
    if transform not in ("location", "sigmoid"):
        _err(f"--transform must be 'location' or 'sigmoid'; got {transform!r}")

    labels = _batch_labels(batches, samples)
    frames = []
    for path, batch in zip(samples, labels):

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