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Add warning to prevent biased transfer when batch effects are missing #394

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Add warning to prevent biased transfer when batch effects are missing #394

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328fd8b
Add warning for fewer batch effects during transfer and Windows compa…
bhumigaddam Mar 12, 2026
405f32e
Resolve merge conflict with dev branch
bhumigaddam Mar 12, 2026
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2 changes: 1 addition & 1 deletion pcntoolkit/dataio/norm_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from __future__ import annotations

import copy
import json
from filelock import FileLock
import os
from collections import defaultdict
from functools import reduce
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9 changes: 9 additions & 0 deletions pcntoolkit/normative_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import importlib.metadata
import json
import os
import warnings
from typing import List, Optional, Tuple, Union

import numpy as np
Expand Down Expand Up @@ -205,6 +206,14 @@ def transfer(self, transfer_data: NormData, save_dir: str | None = None, **kwarg
new_model.response_vars = respvar_intersection

new_model.preprocess(transfer_data)

if hasattr(self, "batch_effects") and hasattr(transfer_data, "batch_effects"):
if len(transfer_data.batch_effects) < len(self.batch_effects):
warnings.warn(
"Transfer dataset contains fewer batch effects than the training dataset. "
"This may lead to biased transfer corrections.",
UserWarning,
)
new_model.register_batch_effects(transfer_data)

Output.print(Messages.TRANSFERRING_MODELS, n_models=len(respvar_intersection))
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