Hi. Thank you in advance. I analyze my flow, actually CyTOF, files (fcs) using R vignettes from Malgorzata Nowicka, eta al. CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets (F1000 article https://f1000research.com/articles/6-748/v3). Everything works great. I have multiple samples from two groups (condition) and sample numbers are different between these two conditions, which results in largely different cell numbers between the two conditions. For instance, one group (condition) has 4 samples with 10000 events each sample. The second group has 10 samples with 10000 events each sample. Combining each group together will have 40000 and 100000 cell events, respectively. After I run: plotDR(sce, "TSNE", color_by = "meta10", facet_by = "condition"), I got a figure with 2 tSNE plots side by side by the 2 conditions. Because one condition has far more events than the other does, the abundance difference of specific clusters can be interpreted by different cell counts. So, I am thinking to make roughly even events from these two conditions. For instance, if 4000 out of 10000 cell counts are analyzed from each sample of condition 2, that will make total events to 40000 (10 samples), which is the equal number to condition 1. As a newbie of R, I just do not know how to do. Please help. Thanks so much.
