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Error in fit$ridge_penalty
Hello again :D
I am getting an error when running test_de(). It is the following one: Error in fit$ridge_penalty : Illegal name after '$' sign: ridge_penalty. Do you have any idea on how to debug it?
The code I am running is the following:
matrix <- assay(sce, "counts")
logmatrix <- shifted_log_transform(matrix)
matrix <- matrix[hvg, ]
logmatrix <- logmatrix[hvg, ]
sce <- SingleCellExperiment(assays = list(counts = matrix, logcounts = logmatrix))
sce$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