goolam.R does not run without error

[benearnthof]

When running goolam.R to convert the data into a SingleCellExperiment line 17 sceset <- create_sce_from_counts(d, ann) causes the following error: Error in .calculate_cpm(assay(x, exprs_values), ...) : unused argument (use.size.factors = FALSE) Traceback information: `Error in .calculate_cpm(assay(x, exprs_values), ...) : unused argument (use.size.factors = FALSE) 9. .local(x, ...) 8. .nextMethod(x = x, size_factors = size_factors, ...) 7. eval(call, callEnv) 6. eval(call, callEnv) 5. callNextMethod(x = x, size_factors = size_factors, ...) 4. .local(x, ...) 3. calculateCPM(sceset, use.size.factors = FALSE) 2. calculateCPM(sceset, use.size.factors = FALSE) at create_sce_mirror.R#14

1. create_sce_from_counts(d, ann) ` R version 3.6.1; This happenes under both Windows 10 and Ubuntu 18.04

[lry199010]

into this function: sceset <- create_sce_from_counts(d, ann) change: exprs(sceset) <- log2(calculateCPM(sceset, use.size.factors = FALSE) + 1) correct: exprs(sceset) <- log2(calculateCPM(sceset) + 1)