Comparison of GOseq and the standard hypergeometric methods. (a)
The P-values generated with GOseq using the Wallenius
approximation and the standard hypergeometric method are plotted
against the P-values calculated with GOseq using random sampling
(200k repeats). The Wallenius method (green crosses) shows good
agreement with the high resolution (200,000 repeats) random
sampling. A large discrepancy in P-values is seen between GOseq
and the hypergeometric method. (a) The number of discrepancies
between lists is shown for a given list size. The black line
compares GOseq using high resolution sampling with the
hypergeometric method. The red line compares GOseq using high
resolution sampling with the Wallenius approximation. Again,
GOseq using the Wallenius method shows little difference from
GOseq using the random sampling method (with 200k repeats) while
the hypergeometric method shows a large number (approximately
20%) of discrepancies. Young et al. Genome Biology 2010 11:R14
doi:10.1186/gb-2010-11-2-r14