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saeyslab / CytoNorm

R library to normalize cytometry data
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cytonorm error in if (any(idx)) { : missing value where TRUE/FALSE needed #43

Open Heather-WHH opened 6 months ago

Heather-WHH commented 6 months ago

Hello,

I ran my samples (n = 10 in total. there are 2 groups, n=5 in each group) over 4 days. I have 1 cytonorm control for each day (total 14 fcs files). I am using cytonorm plugin on flowjo but there is no normalized fcs files generated.

in my step 02 of initial workflow, there seem to be something wrong with my second cytonorm control (and also fourth cytonorm control but I am not sure if both have the same issue). I tried adding emptyValue=F like #37 but there's an error in if (any(idx)) { : missing value where TRUE/FALSE needed This code was in my ROUT file.

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Can you help me please? Thank you

SofieVG commented 6 months ago

I think you will need the truncate_max_range = FALSE

Heather-WHH commented 6 months ago

Hi,

I just added that to this part in step 02: fsom <- CytoNorm::prepareFlowSOM(train_data$Path,truncate_max_range=F, channels, nCells = 6000, FlowSOM.params = list(xdim = 5, ydim = 5, nClus = nCluster, scale = FALSE), #TODO place 'colsToUse' here for user selected params transformList = transformList, seed = 1) it shows me this now: Error in SOM(fsom$data[, colsToUse], silent = silent, ...) : NA/NaN/Inf in foreign function call (arg 1) Timing stopped at: 10.22 0 10.33

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What should I do next?