I ran sce$i <- seq(ncol(sce)) as suggested in #181 (thanks for the suggestion) before exporting the sce into FCS files so that each cell will have a unique numeric value (called nColID).
The output of colData(sce) include this nColID:
In FlowJo, I then gated on some population of interest (and make sure that nColID are only linear transformed so the values don't change by FlowJo), then I exported this gated population as "scale values" csv files and read them into R. I expect each cell in this file should now have a unique nColID, but they are not; some nColID values are duplicated.
My goal is to have a way to pull certain cells from my sce object in R that belong to a gated population that I gated in FlowJo. I looked through the documentations, but did not find the solution. Is it possible with CATALYST?
Hi, Helena,
Thank you for the package.
I ran
sce$i <- seq(ncol(sce))as suggested in #181 (thanks for the suggestion) before exporting thesceinto FCS files so that each cell will have a unique numeric value (called nColID).The output of
colData(sce)include thisnColID:In FlowJo, I then gated on some population of interest (and make sure that nColID are only linear transformed so the values don't change by FlowJo), then I exported this gated population as "scale values" csv files and read them into R. I expect each cell in this file should now have a unique
nColID, but they are not; some nColID values are duplicated.My goal is to have a way to pull certain cells from my
sceobject in R that belong to a gated population that I gated in FlowJo. I looked through the documentations, but did not find the solution. Is it possible withCATALYST?Thank you again for your help.