Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1 | ```
average.fdr(x, breaks)
``` |

`x` |
an object returned by |

`breaks` |
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 `tstat`

and `fdr.local`

.

A. Ploner

Ploner A, Calza S, Gusnanto A, Pawitan Y (2005) Multidimensional local false discovery rate for micorarray studies. *Submitted Manuscript*.

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