This function averages two-dimensional local false discovery rates as computed by
fdr2d for binned values of the first test statistic and across the values of the second test statistic. The result can easily be plotted and should be comparable to the one-dimensional fdr as provided by
fdr1d, provided that the smoothing parameters were chosen suitably.
an object returned by
breaks defining intervals into which the first test statistic is binned; by default the same values that were used by
Assuming that we have smoothed the estimate suitably and have chosen the proportion of non-dffierentially expressed genes suitably, we should get very much the same results from
fdr2d as from
fdr1d when we average across the logarithmized standard errors, see Examples.
The averaging is done across the estimated values for the actual genes; this corresponds to a weighted mean of the smoothed estimates on a grid, where the weight is proportional to cell frequencies.
Note that it is usuually easier to get a good match in the tails of the curves than in the center, which is okay, as this is where we want to estimate the fdr reliably.
A matrix with two columns
Ploner A, Calza S, Gusnanto A, Pawitan Y (2005) Multidimensional local false discovery rate for micorarray studies. Submitted Manuscript.
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