High dimensional immunotyping of the obese tumor microenvironment with unanchored batch correction

Analysis of tumor immune infiltrate in immunocompetent mice with orthotopic syngeneic tumors. This experiment contains 57 fcs files of CD45+ tumor immune infiltrate from 7 CyTOF batches across 5 tumor models in obese and non-obese settings. Files have been normalized and debarcoded. Arcsinh transformation and unanchored cydar range batch correction has been applied to channels with the "c_" prefix. Original channels are present in the files. viSNE tSNE coordinates are also present. Conclusion: Unanchored range-based batch correction using cydar in R was successful and enabled the simultaneous analysis of 7 different CyTOF batches. bioRxiv: https://doi.org/10.1101/2020.10.14.338806 Notes: Breast cancer models: E0771 (2 batches), Wnt1, TeLi Pancreatic cancer: C11 (2 batches), UN-KC High fat diet fed/obese mice: H Standard chow diet/non-obese mice: C Helios CyTOF, Narrow bore (HT) injector Data Normalization