-
Notifications
You must be signed in to change notification settings - Fork 2
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
No genes names when computing devianceFeatureSelection() with batch #25
Comments
Hi @Alexis-Varin, Thanks for the notification about this! I also appreciate the suggested fix, but unfortunately, I wasn't able to verify that it gives the same answers. I implemented your version, but when I ran it on an example object (from the SingleCellExperiment documentation), it gave an odd error message:
Best, |
Hi @kstreet13 ,
The only thing I did was copy your featureSelection.R entire code and only change the
|
Hello,
I am encountering a problem when setting the batch parameter in
devianceFeatureSelection()
, I do not have the gene names associated with the deviance.When doing
I do obtain the genes names ordered by deviance, but when I would like to correct batch effect by adding factor of orig.ident :
The vector is empty, because
rowData(sce)$binomial_deviance
isn't a named numeric vector, just a numeric vector. I guess it comes from the fact that in your code, after computing deviance on each factor level, yourowSums()
the results, but without renaming afterwards.edit :
I fixed it for me using the following modification of
.compute_deviance_batch()
:The text was updated successfully, but these errors were encountered: