Comments (4)
This should be fixed in 205d8b8 - can you reinstall and try again? Note that this now requires tensorflow 2.1.0, readme updated with installation instructions
from clonealign.
Hello, I am having a similar issue. The latest update today did resolve the "no attribute" error, but now I see this.
Error in (function (gene_expression_data, copy_number_data, max_iter = 200, : unused argument (seed = 1392) Calls: run_clonealign -> do.call Execution halted
The Rscript looks like this,
`library(Matrix)
library(tensorflow)
library(clonealign)
#Load Rdata file.
load("HPNE_clonealign.Rdata")
reticulate::py_config()
Sys.getenv()
Sys.unsetenv('VIRTUAL_ENV')
Sys.unsetenv('PATH')
Sys.unsetenv('RETICULATE_REQUIRED_MODULE')
Sys.getenv()
#Fit model.
model_from_clonealign <- run_clonealign(ca_data$gene_expression_data,
ca_data$copy_number_data,
seed = 1392)
#Save.`
from clonealign.
Hi @Toseph
I removed the seed argument to clonealign
so you can now set.seed(...)
beforehand as per bioconductor guidelines.
Thanks,
Kieran
from clonealign.
Thanks for the update @kieranrcampbell! We will test this today and get back to you.
from clonealign.
Related Issues (14)
- Handle situation when copy number is 0
- row dimensionality issue HOT 2
- Performance with multinomial likelihood HOT 9
- size_factors parameter HOT 1
- delta-CN and delta-RNA HOT 1
- the inference runs through one ELBO computation and throws an error (below) if rownames(L) and colnames(Y) don't match or are both NULL.
- when colnames(L) get named in case they are NULL with colnames(Y) <- paste0("gene_", letters[seq_len(ncol(Y))]) wouldn't that give gene_NA if there are more than 26 genes?
- Add test_that for gradient checking
- Different runs upon the same input generated different results HOT 4
- Initial elbo is NA HOT 7
- How to quantify the clonal frequency consistency between DNA and CloneAlign? HOT 2
- Remove outlying genes now multinomial likelihood is used
- Solve the problem in installing clonealign HOT 1
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