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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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T cell Subpopulation Percentage Showing as Zero in Differential Analysis Despite Presence in Clustering Results #401

Closed TongzhenXu closed 2 months ago

TongzhenXu commented 3 months ago

Hi! I am currently working on analyzing my SCE data, specifically focusing on the CD4+ T cell subpopulations. After clustering, my data shows five distinct subpopulations: CD4+ T naive, CD4+ Tcm, CD4+ Tem, CD4+ Temra, CD4+ Teff, and an "Other" group. However, when I proceeded to perform differential analysis on these subpopulations, I noticed an issue.

Despite having successfully identified the CD4+ Temra subpopulation during the clustering step, the subsequent differential analysis shows that the percentage of CD4+ Temra cells is zero in every sample. I am uncertain what could be causing this discrepancy, as the CD4+ Temra subpopulation was clearly present in my initial clustering results.

Could you please help me understand why the percentage of CD4+ Temra cells is being reported as zero in the differential analysis? Any insights or suggestions for troubleshooting this issue would be greatly appreciated.

Thank you for your assistance.

Best regards, Tongzhen

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HelenaLC commented 3 months ago

This is more of an issue for diffcyt than CATALYST, these are different packages. Things look like they show up correctly in the plot you posted. Please post the issue to diffcyt, as I’m not sure what might be causing NA p-values.