Starlitnightly
commented
2 weeks ago This doesn't seem to be a code ERROR, but a boundary check ERROR, the following answer is from GPT for reference:
The error you're encountering with the ov.single.batch_correction function when setting n_pcs (number of principal components) to less than 13 in your code is due to a mismatch between the number of principal components and the requirements of the Harmony integration process. Let's break down the possible reasons and solutions for this issue:
Understanding the Error
-
Principal Component Analysis (PCA):
- PCA is used to reduce the dimensionality of the dataset while preserving as much variability as possible.
- When you set
n_pcs=12, it means that the PCA will reduce the dataset to 12 principal components.
-
Harmony Integration:
- Harmony is used for batch effect correction in single-cell RNA-seq data.
- The
harmony_integratefunction from thescanpypackage is called to perform this integration using the specified principal components.
-
Error Source:
- The error indicates a
ValueErrordue toNaNvalues encountered during the KMeans clustering step inside the Harmony algorithm. - This suggests that reducing
n_pcsto less than 13 might be leading to issues such asNaNvalues or an insufficient number of features for clustering.
- The error indicates a
Possible Reasons for the Error
-
Insufficient Dimensionality:
- Reducing the number of principal components to less than a certain threshold (in your case, 13) might lead to an insufficient number of features to capture the essential variability of the dataset.
- Harmony and KMeans clustering can struggle with too few features, leading to unstable or ill-defined clustering solutions.
-
Data Quality Issues:
- With fewer components, the PCA-transformed data might include
NaNor near-zero variance components, which are problematic for subsequent steps in Harmony's algorithm.
- With fewer components, the PCA-transformed data might include
-
Specific Implementation Requirements:
- The Harmony integration process might have internal checks or requirements for a minimum number of principal components to function correctly.
Solutions
-
Increase
n_pcs:- Ensure that
n_pcsis sufficiently high to capture the variability in the dataset. In your case, settingn_pcsto at least 13 seems to work. - You can try different values above 12 to find the minimum number of components that prevent the error.
- Ensure that
-
Check for NaNs:
- Before running Harmony, inspect the PCA output to ensure there are no
NaNvalues. - You can use
numpyorpandasto check for and handleNaNvalues in your dataset.
import numpy as np import pandas as pd # Assuming adata is your AnnData object pca_output = adata.obsm['X_pca'] if np.isnan(pca_output).any(): print("NaN values found in PCA output") - Before running Harmony, inspect the PCA output to ensure there are no
-
Review Harmony's Requirements:
- Review the Harmony documentation and requirements to ensure your settings and inputs align with its expected usage.
- Harmony might require a certain number of principal components to function effectively.
-
Data Preprocessing:
- Ensure that the data preprocessing steps (scaling, normalization, etc.) are correctly applied before running PCA and Harmony.
Example Code Adjustment
Here's how you might adjust your code to ensure it works properly:
import ov
import scanpy as sc
# Check if PCA output has NaNs
adata3 = adata.copy()
sc.pp.scale(adata3) # Example scaling step
sc.tl.pca(adata3, n_comps=12) # Trying with 12 principal components
if np.isnan(adata3.obsm['X_pca']).any():
raise ValueError("PCA output contains NaNs, increase n_pcs or preprocess data")
# Now perform batch correction
adata_harmony = ov.single.batch_correction(adata, batch_key='batch', methods='harmony', n_pcs=15)Summary
The error arises due to issues related to the dimensionality reduction step (PCA) when the number of components (n_pcs) is too low for Harmony's integration to handle properly. To resolve this, try increasing n_pcs to a higher value, ensuring that there are no NaN values in the PCA output, and checking Harmony's requirements for the number of principal components.
liuxiawei
Describe the bug When I use code like following with npcs lower than 13 (like 12), it make error
Error msg:
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