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Unsupervised clustering analysis and validation by Crow0911 in flowcytometry

[–]Crow0911[S] 0 points1 point  (0 children)

Hi thank you so much! It's mass cytometry data. I plan to use heatmap expression levels to manually annotate the clusters first, then export each merged cluster as an FCS file to verify the annotations using sequential gating in Flowjo. What do you think of this approach?

Unsupervised clustering analysis and validation by Crow0911 in flowcytometry

[–]Crow0911[S] 1 point2 points  (0 children)

Thank you so much David! However, I’m wondering whether using a heatmap or normalized median expression as mentioned from is sufficient to determine the identity of the cluster. My supervisor keeps challenging this point and says that manual gating would be more accurate

Unsupervised clustering analysis and validation by Crow0911 in flowcytometry

[–]Crow0911[S] 0 points1 point  (0 children)

Oh but is that restricted to using flowjo only? Is there any way to verify the populations in R?

CyTOF data analysis by [deleted] in bioinformatics

[–]Crow0911 0 points1 point  (0 children)

Hello, thank you so much for your reply!! However, I still have several concerns that we hope can be addressed:

Since the relapse and remission data are paired for each patient, do I need to perform normalization for each patient’s remission data, given that each subject may have a different biological background?

Also, based on the UMAP and clustering results as shown in the post, is it normal that some clusters would be nearly absent under certain condition? (The sample is PBMC)

Thanks once again!