Figure 1.
Schematic diagram of a flow cytometer, showing focusing of the fluid sheath, laser, optics (in simplified form, omitting focusing), photomultiplier tubes (PMTs), analogue-to-digital converter, and analysis workstation.
Figure 2.
An example pipeline for analysis of FCM data and some of the Bioconductor packages relevant to each step.
Figure 3.
Comparison of consensus of eight independent manual gates (polygons) and automated gates (colored dots).
The consensus of the manual gates and the algorithms were produced using the CLUE package [25]. Figure reproduced with permission from [26].
Figure 4.
Cell populations in a high-dimensional mass-cytometry dataset manually gated after dimension reduction using 2-D layout for a minimum spanning tree.
Figure reproduced from the data provided in [40].
Figure 5.
An example of probability binning, created using the flowFP Bioconductor package.
The dots represent individual events in an FCS file. The rectangles represent the bins.
Figure 6.
Overview of the flowType/RchyOptimyx pipeline for identification of correlates of protection against HIV.
First, tens of thousands of cell populations are identified by combining one-dimensional partitions (panel 1). The cell populations are then analyzed using a statistical test (and Bonferroni's method for multiple testing correction) to identify those correlated with the survival information. Panel 3 shows a complete gating hierarchy describing all possible strategies for gating that cell population. This graph can be mined to identify the “best” gating strategy (i.e., the one in which the most important markers appear earlier). These hierarchies for all selected phenotypes are demonstrated in panel 4. In panel 5, these hierarchies are merged into a single graph that summarizes the entire dataset and demonstrates the trade-off between the number of markers involved in each phenotype and the significance of the correlation with the clinical outcome (e.g., as measured by the KaplanMeier estimator in panel 6). Figure reproduced in part from [49] (public domain) and [50].
Figure 7.
Representation of flow cytometry data from an instrument with three scatter channels and 13 fluorescent channels.
Only the values for the first 30 (of hundreds of thousands) of cells are shown.