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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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Using filter(): Umap function doesn't work #65

Closed bioguy2018 closed 4 years ago

bioguy2018 commented 4 years ago

Hello, I have subsetted my data using the filter() function but apparently it cause some problems in the SummarizedExperiment slots because I get the following error:

Error in validObject(x) : invalid class “daFrame” object: 'elementMetadata' slot must contain a zero-column DataFrame at all time

also the clustering doesn't work anymore on the subset dataset with the following error:

o running FlowSOM clustering... o running ConsensusClusterPlus metaclustering... Error in [[<-(*tmp*, name, value = c(276L, 185L, 216L, 188L, 233L, : 99839 elements in value to replace 0 elements

I am using version 1.8.7 of catalyst

any idea how to resolve it? it is quite urgent to me :(

bioguy2018 commented 4 years ago

Okay, like previous times I also solved this problem by avoiding using filter() function and subset the environment in the traditional way using which() ! daf[which()]