SEQanswers TMM normalization examplified and explained
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 11-11-2014, 12:05 AM #1 LeonDK Member   Location: Denmark Join Date: Sep 2014 Posts: 69 TMM normalization examplified and explained So according to the Robinson's 2010 paper on TMM normalization, the calculation of TMM factors, is given by: If we then take this hypothetical count matrix: Code: ``` 1 2 3 4 5 a 711 662 138 424 604 b 247 879 547 406 230 c 390 891 678 919 967 d 92 567 529 809 605 e 963 594 87 541 640 f 11 365 620 108 919 g 575 358 32 455 148 h 765 592 462 52 330 i 874 866 331 759 733 j 42 681 634 84 681``` Could anyone briefly exemplify how to perform the calculation of the TMM factors manually? I realise, that I can the normalization factors like so: Code: ```R library(edgeR) set.seed(13) counts = as.data.frame(matrix( floor(runif(10*5,1,1001)), 10, 5)) rownames(counts) = letters[1:10] colnames(counts) = seq(1,5) d = DGEList(counts=counts) d = calcNormFactors(d,method="TMM”) d\$samples\$norm.factors [1] 0.9412422 0.9510114 0.9604313 1.1794450 0.9862088``` But i'd love to do a manual calculation, to understand the details of exactly how the TMM values are calculated Cheers, Leon
 11-11-2014, 12:49 AM #2 dpryan Devon Ryan   Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,479 Just look at the code for calcNormFactors. I recall it being fairly short.