const-ae / const-ae/lemur

Error in fit$ridge_penalty

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Description

Hello again :D

I am getting an error when running `test_de()`. It is the following one: `Error in fit$ridge_penalty : Illegal name after '$' sign: ridge_penalty`. Do you have any idea on how to debug it?

The code I am running is the following:

```r
matrix <- assay(sce, "counts")
logmatrix <- shifted_log_transform(matrix)
matrix <- matrix[hvg, ]
logmatrix <- logmatrix[hvg, ]
sce <- SingleCellExperiment(assays = list(counts = matrix, logcounts = logmatrix))
sce$condition <- condition
sce$sample <- sample
fit <- lemur(sce, design = ~ sample + condition, n_embedding = 20, test_fraction = 0.25)
fit <- test_de(fit, contrast = cond(condition = "cond2") - cond(condition = "cond1"))
```

I've tried with both the BiocManager version 3.18 and with the GitHub devel installation (version 1.1.9).

Best,

Pedro

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