Thomas Ashhurst comments

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                                            Thomas Ashhurst

nClus parameter not working

@emmanuelaaaaa that tmp folder thing is a subtle trap, so well done for noticing it! Always worth checking to see if it's still there, which might happen if CytoNorm gets...

Error in rep(NA, (width - length(x))) : invalid 'times' argument

@SansMorel I came up with the same error. After pulling the function apart, the first problem comes up in this part of `testCV`, at the end of the function: `res

Error in rep(NA, (width - length(x))) : invalid 'times' argument

So yes, it carries the `cluster_values` value the whole way through to that point. If you change it fro `c(5, 10, 15)` to `c(5, 10)` then it works fine.

Infinite max range on normed FCS files

@emmanuelaaaaa @emrizzi @SofieVG this is interesting. @ghar1821 and I have occasionally found the odd couple of cells that have been given extremely high values (or extremely high negative values) after...

Could CytoNorm impede discovery of novel clusters?

@vivek-verma202 it doesn't have to, but it's a bit complicated. In our implementation in [Spectre](https://sydneycytometry.org.au/spectre) we generate clusters using only stable markers to get the major population groups (e.g. Ly6G,...

FlowSOM fail on new normalized FCS files

@EAC-T you can also try using fewer metacluster to try and generate a slightly more accurate model -- this can often help prevent those extremely high values appearing the resulting...

Discovery workflow with batch alignment using CytoNorm -- link broken

Ah apologies that’s our fault, will update it shortly — but here is the actual link: https://unisyd-my.sharepoint.com/personal/thomas_ashhurst_sydney_edu_au/_layouts/15/onedrive.aspx?id=%2Fpersonal%2Fthomas%5Fashhurst%5Fsydney%5Fedu%5Fau%2FDocuments%2FShared%2FSpectre%20PDFs%2FDiscovery%20workflow%20with%20batch%20alignment%20using%20CytoNorm%2Dv19%2D20240415%5F044409%2Epdf&parent=%2Fpersonal%2Fthomas%5Fashhurst%5Fsydney%5Fedu%5Fau%2FDocuments%2FShared%2FSpectre%20PDFs&ga=1 Tom ________________________________ From: Marie Crane ***@***.***> Sent: Tuesday, May 14, 2024 16:13 To:...