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SofieVG / FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data
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SaveClustersToFCS #23

Open roskcl opened 5 years ago

roskcl commented 5 years ago

Hello,

I have used SaveClustersToFCS and imported the newly created .fcs files in R or flowjo. When I then check the node information added in the FlowSOM column with either of the softwares I would expect that each cell had a value between 1 and 100 as I had 100 nodes in my FlowSOM run.

However, this are the values that I am obtaining:

unique(exprs(fcs[[1]]$FlowSOM)) FlowSOM [1,] 10 [2,] 8 [3,] 96 [4,] 47 [5,] 3 [6,] 65 [7,] 2 [8,] 9

Could you help me understand where these values come from? Also, I would rather link the information of the metaclusters than the nodes. Is this possible?

Thank you very much for your help!

SofieVG commented 3 years ago

Dear @RosaKCL

My apologies about the very late answer. I would guess the issue with the limited number of clusters was that in some way the data had such a specific structure that you had many empty clusters in the mapping?

We just added the metaclusters to the fcs files now as well, thanks for this suggestion. Note that there have been some major changes in the updates from the last months, so it might be necessary to make small adaptations in your previous script.

Kind regards, Sofie