SPICE: exploration and analysis of post-cytometric complex multivariate datasets.
Polychromatic flow cytometry results in complex, multivariate datasets. To date, tools for the aggregate analysis of these datasets across multiple specimens grouped by different categorical variables, such as demographic information, have not been optimized. Often, the exploration of such datasets is accomplished by visualization of patterns with pie charts or bar charts, without easy access to statistical comparisons of measurements that comprise multiple components. Here we report on algorithms and a graphical interface we developed for these purposes. In particular, we discuss thresholding necessary for accurate representation of data in pie charts, the implications for display and comparison of normalized versus unnormalized data, and the effects of averaging when samples with significant background noise are present. Finally, we define a statistic for the nonparametric comparison of complex distributions to test for difference between groups of samples based on multi-component measurements. While originally developed to support the analysis of T cell functional profiles, these techniques are amenable to a broad range of datatypes.
Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA. Roederer@nih.gov
Mario
M
Roederer
Joshua L
JL
Nozzi
Martha C
MC
Nason
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003627:Data Interpretation, Statistical; D005434:Flow Cytometry / Q000379:methods*; D006801:Humans; D015999:Multivariate Analysis; D025341:Principal Component Analysis / Q000379:methods; D012984:Software
PLoS One. 2010 Jun 21;5(6):e11237
20574540
PLoS Pathog. 2009 Feb;5(2):e1000295
19214220
Immunology. 2008 Dec;125(4):441-9
19137647
J Immunol. 2010 May 1;184(9):4926-35
20363974
Nat Med. 2006 Aug;12(8):972-7
16862156
Cytometry A. 2008 Nov;73(11):975-83
18785267
Cytometry. 1996 Jul 1;24(3):191-7
8800551
PLoS One. 2010 Feb 02;5(2):e9015
20126394
Nat Med. 2007 Jul;13(7):843-50
17558415
Blood. 2009 Mar 5;113(10):2238-44
18997173
Cytometry A. 2010 Jul;77(7):705-13
20583274
Nat Rev Immunol. 2004 Aug;4(8):648-55
15286731
AIDS. 2010 Apr 24;24(7):947-57
20179574
PLoS One. 2010 Mar 24;5(3):e9852
20352042
Nat Rev Immunol. 2008 Apr;8(4):247-58
18323851
Blood. 2009 Apr 23;113(17):3978-89
19109229
Cytometry A. 2010 Jul;77(7):614-22
20583275
Eur J Immunol. 2008 Feb;38(2):350-63
18200635
J Immunol. 2010 Jun 1;184(11):6537-44
20435929
J Exp Med. 2007 Oct 1;204(10):2473-85
17893201
Blood. 2006 Jun 15;107(12):4781-9
16467198
J Immunol. 2002 Dec 1;169(11):6376-85
12444145
Cytometry A. 2008 Sep;73(9):868-74
18629844
J Virol. 2008 Sep;82(17):8812-9
18579590
Blood. 2004 Feb 1;103(3):966-72
12958069