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seasamgo / rescue

Bootstrap imputation for scRNAseq data
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impute Error #7

Closed Adominguez-pact closed 4 years ago

Adominguez-pact commented 4 years ago

Hello,

Following the tutorial, I get this error when running the impute portion

impute <- rescue::bootstrapImputation(expression_matrix = expression_dropout@assays$RNA@data)
Error in :=(covariance, (stdev/mean_expr)) : could not find function ":="

any ideas?

RubD commented 4 years ago

Hi,

It looks like the data.table package was not loaded.

Calling library(data.table) first might fix the issue.

RubD commented 4 years ago

Hi,

It looks like the data.table package was not loaded.

Calling library(data.table) first might fix the issue.

This did not fix the issue, but I have updated the package and now the tutorial should work again. It was a namespace issue.

FYI, currently it's a good idea to explicitly provide the python path to the function bootstrapImputation. This is the path where you have installed the necessary python modules.