Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error in fit$ridge_penalty #14

Open
BiotechPedro opened this issue Apr 4, 2024 · 0 comments
Open

Error in fit$ridge_penalty #14

BiotechPedro opened this issue Apr 4, 2024 · 0 comments

Comments

@BiotechPedro
Copy link

BiotechPedro commented Apr 4, 2024

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant