Thomas Ashhurst

Hey mate! The first issue is odd as it works fine on my laptop, however, there is an issue in the code that might be the problem: `deets

@denvercal1234GitHub is there any chance the X and Y are flipped between the FlowJo and R examples? There is a string of cells on the bottom right that looks similar...

@denvercal1234GitHub just looking back over some of these issues -- @SamGG's image summarises it well, and this is also described in our transformation tutorial (https://immunedynamics.io/spectre/cytometry/#tutorials). Personally having run clustering on...

Hi @denvercal1234GitHub hmm I get this on occasion -- the issue is to do with the UMAP calculations, which should be independent from FlowSOM clustering (i.e., even if you change...

@denvercal1234GitHub sorry for the delayed reply here -- essentially an nxn plot -- so CD3 vs CD4, CD3 vs CD19, CD3 vs N etc. In each, plotting the metacluster. You...

Cool idea!

@ghar1821 spot on! @denvercal1234GitHub normalisation will run on the columns, regardless of whether it has been transposed or not.

Hi @denvercal1234GitHub **QUESTION 1. As a result, if a package requires the data to be transformed, should I skip data transformation (e.g., flowCore::transform()) once I converted the channel values into...

@mabar1 there is actually an argument in the write.hdf5 function that will allow you to create a merged channel, using whichever combination of channels you like. ```write.hdf5(dat = spatial.dat, channels...

@mabar1 that is actually pretty unusual. Are you using IMC data?