feature selection method using pearson residuals discrepancies

[jflucier]

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What happened?

Hi,

I have performed multiple way to do features selection using pearson residuals and methods return different results.

Method 1 plot:

Method 2 plot:

I dont understand why these 2 methods dont produce the same result.

Based on those graph I think the best is method 2 but would like to understand why these dont produce similar plots.

Thanks in advance for your help

Minimal code sample

### 1st method:
analytic_pearson = sc.experimental.pp.normalize_pearson_residuals(adata, inplace=False)
adata.layers["analytic_pearson_residuals"] = csr_matrix(analytic_pearson["X"])
sc.pp.highly_variable_genes(adata, layer="analytic_pearson_residuals", n_top_genes=4000)
ax = sns.scatterplot(
data=adata.var, x="means", y="dispersions", hue="highly_variable", s=5
)

## 2nd method:

fig, ax = plt.subplots(1, 1, figsize=(10, 5))
sc.experimental.pp.highly_variable_genes(
adata, flavor="pearson_residuals", n_top_genes=4000
)
ax = sns.scatterplot(
data=adata.var, x="means", y="dispersions", hue="highly_variable", s=5
)
ax.set_xscale("log")
ax.set_yscale("log")
ax.set_title("Feature selection using Pearson residuals normalisation (from highly_variable_genes flavor pearson_residuals)")
pdf.savefig(bbox_inches="tight")

Error output

Versions

[jflucier]

Another observation.

If I run scry on same data, I get this plot:

The same plot but using highly_variable_genes suing flavor pearson_residuals:

Though the pearson_resdual flavor was a reimplementation of scry but maybe I got this wrong.

Thanks for your help understanding this

[flying-sheep]

Hi, good question! I’m not super up-to-date with this corner of scanpy.

There’s a PR by @ktpolanski that implements the deviance method from scry: #1765

I’ll investigate the state of the experimental functions and that PR and see how we can best move forward.

I think @jlause implemented the scry method in #1715, but as said, I haven’t looked into it at all yet.

[flying-sheep]

also relevant: #2176