Cluster median data for individual samples

[ghost]

I generated FlowSOM clusters in cytofkit for 20 samples and would like to view the median expression of each cluster for each sample in a CSV file, not every sample together. Is there a way to do this? When I select individual samples on the left it seems to overwrite the file and not create a new one.

[SamGG]

Hi, FlowSOM is clustering algorithm that makes homogeneous groups. So the cells in a cluster share a similar expression profile. As such, there should not be differences among cells in a cluster. If selecting a sample leads to a different content of the CSV file, maybe you should rename the CSV file after having saved it. Best.

[ghost]

Hello, sorry what I meant to say is after I run the flowSOM clustering for 20 samples, I get only one CSV file named cluster_median_data showing the expression of each marker for each cluster. What I want is 20 CSV files, one for each sample, showing expression of each marker for each cluster. Is there a way to do this?

[SamGG]

Did you try to select one sample in the left part of the interface, then save, then rename the median file, then select another single sample, then save, then compare the two CSV file. If values are exactly the same, then this one-by-one sample selection approach does not work. If there are some small difference, the approach is working. Don't forget, clusters are based on the intensity of the selected markers for flowSOM. So the median values will be nearly the same. But the median values of the unselected markers should be different. I don't know if you are interested in the latter.

[ghost]

It gave exactly the same values for selected and unselected markers.....but thank you for your help.

[SamGG]

Do you have a few knowledge of R?

[ghost]

I know how to import data and plot some graphs, but not clustering. I'm very keen to learn it. Please let me know what I should do.

[SamGG]

I will do some trials to guess the easy way.