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JinmiaoChenLab / cytofkit

cytofkit: an integrated flow/mass cytometry data analysis pipeline
http://jinmiaochenlab.github.io/cytofkit/
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Read.flow.Set error #93

Closed nayaracleite closed 2 years ago

nayaracleite commented 2 years ago

Hello,

I'm getting this error when I try to load the .FCS files:

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Warning in readFCSdata(con, offsets, txt, transformation, which.lines, scale, : Some data values of 'Er167Di' channel exceed its $PnR value 12000 and will be truncated! To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'

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Do you have any idea how to fix it?

Thank you Nayara

SamGG commented 2 years ago

Hi, You might find more support on cytofkit2. Nevertheless cytofkit2 didn't correct this error.

To solve it you have to change the code at https://github.com/JinmiaoChenLab/cytofkit/blob/3d134085453231403a3cf327e981b419f966295c/R/cytof_preProcess.R#L131 and https://github.com/JinmiaoChenLab/cytofkit/blob/3d134085453231403a3cf327e981b419f966295c/R/cytof_preProcess.R#L133 and replace FALSE) by FALSE, truncate_max_range = FALSE)

Alternatively, you could try my own fork in which I already corrected this problem. https://github.com/i-cyto/cytofkitlab

HTH, Samuel

nayaracleite commented 2 years ago

Awesome, it worked! Thank you.