alphapepttools.pp.irs

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alphapepttools.pp.irs#

alphapepttools.pp.irs(adata, group_column, reference_column=None, reference_value=None, *, layer=None, inplace=True)#

Internal Reference Scaling (IRS) normalization.

Normalize features across multiple runs (e.g. TMT plexes) using a shared internal reference, as commonly performed in isobaric labelling experiments [PWZ+17]. For each run defined by group_column, a per-feature reference profile is computed from the samples where reference_column == reference_value. Every sample in that run is then rescaled so its reference profile matches the geometric mean of reference profiles taken across all runs. NaNs are propagated.

If reference_column is None, the per-run arithmetic mean across all samples is used in place of an explicit reference.

Parameters:

  • adata (AnnData) – AnnData object

  • group_column (str) – Column in adata.obs that defines the individual runs.

  • reference_column (str | None (default: None)) – Column in adata.obs indicating which samples are reference channels. If None, a virtual reference is constructed from the arithmetic mean of all samples within each run.

  • reference_value (object | None (default: None)) – Value in reference_column that marks the reference sample(s) within each run. Ignored when reference_column is None.

  • layer (str | None (default: None)) – Layer in adata to normalize. If None, uses adata.X.

  • inplace (bool (default: True)) – If True (default), modifies adata inplace and returns None. If False, returns a modified copy of adata.

  • copy –

    Deprecated since version 0.5.0: Use inplace instead. copy will be removed in version 0.6.0.

Return type:

AnnData | None

Returns:

AnnData object with IRS-normalized layer. If inplace=True modifies the anndata object at layer inplace and returns None. If inplace=False, returns a modified copy.

  • Plubell, D. L. et al. Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue. Mol Cell Proteomics 16, 873-890 (2017).

  • Phillip Wilmarth. Thorough Testing of Internal Reference Scaling (IRS) [Website]. https://pwilmart.github.io/TMT_analysis_examples/IRS_validation.html. (2019)

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