Does Cross-Panel Pretraining Transfer Under Marker Heterogeneity? A Large-Scale Empirical Study in Clinical Flow Cytometry

Flow cytometry is the primary assay for single-cell immune profiling, yet cross-study modelling remains under-explored. The challenge is two-fold: Studies measure different marker panels, inducing feature-space inconsistency, while batch effects shift signals even on shared markers, making transfer harder than in vision or language where input spaces are stable. We conduct a large-scale empirical study, pretraining an encoder on 89,324 samples from 112 public studies spanning 525 distinct marker panels. We evaluate it frozen --- isolating representation quality from task-specific adaptation, on five clinical tasks under a taxonomy of panel-overlap conditions, including three panel-zero-shot tasks whose marker panels were unseen during pretraining, and one negative control with no expected discriminative signal. We further characterise transfer across scaling axes and probe robustness to marker removal at test time. Despite heterogeneity that disrupts direct transfer, the frozen encoder matches or exceeds in-distribution specialist encoders on 4 of 5 tasks, including all three novel-panel tasks, and behaves as expected on the negative control. Scaling analyses reveal saturation in both encoder capacity and random corpus subsampling, and representations degrade gracefully under marker reduction. These results suggest a pretrained encoder can serve as a general-purpose feature extractor for clinical cytometry data, without task-specific retraining.