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No control over number of PCs in batch_correct_none #307

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wlason opened this issue Aug 13, 2024 · 1 comment · May be fixed by #312
Open

No control over number of PCs in batch_correct_none #307

wlason opened this issue Aug 13, 2024 · 1 comment · May be fixed by #312
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@SarahOuologuem

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@wlason
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wlason commented Aug 13, 2024

I have a complex study design with not all antibodies present in every sample (there are 24 in total).
I would like to run protein batch correction using harmony with 10 PCs, the number of PCs gets correctly parsed to harmony, but not to no correction workflow, resulting in an error.

ValueError: n_components=20 must be between 1 and min(n_samples, n_features)=19 with svd_solver='arpack'

panpipes/panpipes/python_scripts/batch_correct_none.py

Lines 96 to 99 in 0bc49a4

if adata.var.shape[0] < n_pcs:
L.info("You have less features than number of PCs you intend to calculate")
n_pcs = adata.var.shape[0] - 1
L.info("Setting n PCS to %i" % int(n_pcs))

There is no way to change the default n-1 in the yaml.
@wlason
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wlason commented Aug 13, 2024

The workaround is to specify the number of PCs in the preprocessing yaml. Maybe it can be added to the documentation.

panpipes/panpipes/panpipes/pipeline_preprocess/pipeline.yml

Lines 172 to 173 in 0bc49a4

pca: False
n_pcs: 50

@SarahOuologuem SarahOuologuem self-assigned this Aug 28, 2024
@SarahOuologuem SarahOuologuem linked a pull request Sep 3, 2024 that will close this issue
Fix #307 #312
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Fix #307 DendrouLab/panpipes
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@wlason @SarahOuologuem