FlowJo Data Analysis Software Operation

severe

Rare Cell Population Incorrectly Gated or Missed

Target rare immune cell subsets (e.g., dendritic cells, innate lymphoid cells, hematopoietic progenitors) appear overestimated or masked by abundant terminally differentiated cells. Gating on single markers yields incorrect population percentages (e.g., 4.5% vs. true 1.2% DCs).

💡 4 · ✓ 4

severe

Inappropriate Control Type Selected for Experiment

Control used does not address the main source of background in the experiment, leading to incorrect gating and data interpretation. Results are inconsistent or unreliable despite using controls.

💡 4 · ✓ 5

moderate

Autofluorescence Complicating Cell Population Gating Strategy

Difficult to establish clear gates between positive and negative populations. Autofluorescent cells appear in unexpected regions of scatter plots, creating ambiguous boundaries and potential misidentification of cell populations.

💡 4 · ✓ 5

moderate

High Background in Biological Control Sample

Biological control (e.g., unstimulated sample in stimulation assay) shows unexpectedly high background, making it difficult to set clear positive/negative boundaries.

💡 4 · ✓ 5