Warning messages:
1: In .disambiguate_args(...) :
non-plotting arguments like 'pca_data_input' should go in 'run_args'
2: 'return_SCE=TRUE' is deprecated, use 'runPCA' instead
And the dots in the PCAplot were not colored according to outliers or not.
My R version is 3.5 and scater package version is 1.8.0.
Hi, I copy the code in http://hemberg-lab.github.io/scRNA.seq.course/cleaning-the-expression-matrix.html#exprs-qc and try plotPCA for automatic cell filtering. I put the code "assay(umi, "logcounts") <- log2(counts(umi) + 1)" before running plotPCA and the warning message is like this
Warning messages: 1: In .disambiguate_args(...) : non-plotting arguments like 'pca_data_input' should go in 'run_args' 2: 'return_SCE=TRUE' is deprecated, use 'runPCA' instead
And the dots in the PCAplot were not colored according to outliers or not. My R version is 3.5 and scater package version is 1.8.0.
Thanks!