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Compensation export


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We have analysed around 400 patient samples (with 19 x 10-13 color panels). We'd like to use the .fcs files for downstream cluster analyses (viSNE, PhenoGraph, SPADE etc.)

We experienced some previously unnoticed and very obvious compensation artifacts in some of the files which we'd like to correct. I am aware that this is not ideal. However, since most of the samples were very precious and most of them already consumed, we can't measure them again.

The easiest way for us would be an export function for .fcs files from Kaluza .analysis files. As I understand, the .analysis files are a "container" for the .fcs files, however when extracting the .fcs files from the .analysis files (e.g. via 7zip) the (updated) compensation seems not to to be stored in the $SPILLOVER keyword or at all.

Our workaround now is to save the compensation as .txt file and to apply them to the original .fcs via R scripts or to manually transfer the values to a new flowjo compensation matrix. This is of course very tedious, hence the question.

We hope this is nothing that we'd have to do repeatedly, however an export function in Kaluza would be very very beneficial for multifold purposes.

 

Best,

Timo

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Thanks for the explanation, that does make sense.

 

Kaluza, for better or worse, has a very strict "never modify the listmode" rule. So when you adjust compensation what Kaluza does is to store your original listmode as well as information about how you want to view it, including any compensation adjustments. So your compensation values are saved; they're in the XML that accompanies the listmodes.

 

It would be technically possible to pull the information out of the XML file but it's pretty complicated. Unless you have access to a talented programmer, the path of least work is probably to do what you're already doing for each file.

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