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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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MDS plot #392

Closed galvaresborges closed 1 month ago

galvaresborges commented 3 months ago

I am encountering an error when trying to generate the MDS plot on the Bodenmiller dataset, following the CyTOF workflow (https://bioconductor.org/packages/release/workflows/vignettes/cytofWorkflow/inst/doc/cytofWorkflow.html). The error message is:

pbMDS(sce, color_by = "condition", label_by = "sample_id")

Error: [matrixStats (>= 1.2.0)] useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. See also ?matrixStats::matrixStats.options

Could someone please help me resolve this issue?

emoussay commented 1 month ago

Hi, I had the same issue. Remove matrixStats and install the older 1.1 version. Solved the problem for me Hope this helps

HelenaLC commented 1 month ago

Yeah, I believe this isn't a CATALYST issue as all examples and unit tests are running smoothly; closing for now, but happy to pick it up if it remains an issue.