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Flow cytometry data sets from clinical trials generate very large data sets and are usually highly standardized. Staining variability of individual makers is not uncommon and complicates manual gating, requiring the analyst to adapt gates for each sample. There are also others sources of technical variation, ranging from slight differences in sample handling and preparation to instrument drift between runs. Although great pains are taken by operators to reduce these, small variations may still exist. It can lead to unreliable measurements, especially if a template-gating approach is used without further correction to the gates. Some techniques was developed for normalizing the fluorescence intensity of multiple markers in specific cell populations across samples, that is suitable for high-throughput processing of large, clinical trials data sets.
(Finak et al., 2014) High-throughput flow cytometry data normalization for clinical trials. Cytometry A.
(O'Neill et al., 2015) Deep profiling of multitube flow cytometry data. Bioinformatics.