Flow data: previously transformed fcs

kevinblighe / scDataviz

scDataviz: single cell dataviz and downstream analyses

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Flow data: previously transformed fcs #24

Closed tdfy closed 2 years ago

tdfy commented 2 years ago

Hello,

I am working with fcs files that have already been scaled/normalized. For each marker in the fcs file there is the raw, scaled, scaled/normalized equivalent. When executing 'processFCS' for downstream dimension reduction and visualization, is it possible to select transformed parameters while having 'transformation = FALSE'? Thank you.

-Todd

tdfy commented 2 years ago

Got this sorted. Follow flowCore docs for readFCS function, applied comparable processFCS "colsRetain". https://www.bioconductor.org/packages/devel/bioc/vignettes/flowCore/inst/doc/HowTo-flowCore.pdf