question with extractClusters function

[jenkinmt]

hello, I am trying to export clusters as fcs files for subsequent analysis in cytobank. my experiment metadata had 10 total mice in 2 genotypes, with 6 different stimulations. however when i extracted clusters to fcs, it did not split them up based on the metadata but rather just lumped all the cells from each metacluster together. is there a way to write each cluster as an fcs file for each experimental condition?

Thanks Matt Jenkins

[SamGG]

Hi, I don't have the answer. I am just curious why you want to go back to cytobank? what subsequent analysis do you think about? Best.

[jenkinmt]

Hi, I am wanting to do some cluster gating to assess signaling responses to cytokines based on % in gate for pstat1, pstat3, etc etc within my clusters. thanks Matt

On Jan 17, 2023, at 12:22 PM, Samuel Granjeaud @.**@.>> wrote:

Hi, I don't have the answer. I am just curious why you want to go back to cytobank? what subsequent analysis do you think about? Best.

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[SamGG]

Thanks for your feedback. While MFI might be a way to identify a change in a state/signling marker, I am convinced that gating is more sensitive and informative. a) Did you try to include the signaling markers in the clustering step (FlowSOM I guess) in order to automate the pos/neg separation? b) I think sce could be split in a list of 2 sce according the condition column data. c) Take a look at sce2fcs() as it allows to split the sce object into a flowSet using a split parameter chosen from colData(sce). Maybe it could help. There is an example at https://github.com/HelenaLC/CATALYST/issues/181#issuecomment-1057821016 d) your current probably have a cluster_id column that might allow you to gate and extract the desired clusters. Hope this help while waiting for Helena's answer. Best PS: could you edit your previous reply in order to keep the thread clean. Thanks.

[HelenaLC]

Closing due to inactivity.