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:
Could anyone briefly exemplify how to perform the calculation of the TMM factors manually?
I realise, that I can the normalization factors like so:
But i'd love to do a manual calculation, to understand the details of exactly how the TMM values are calculated
Cheers,
Leon
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
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
Cheers,
Leon
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