| LocalFDR {anapuce} | R Documentation |
Local FDR
Description
Estimation of local false discovery rates
Usage
LocalFDR(dataf = dataf, graph = TRUE, method = NULL, lambda0 = 0.5,
smoothing = "1", thres = c(0.01, 0.05, 0.1, 0.2), mm = c(3, 5, 15, NA))
Arguments
dataf |
input data file with two columns (1 = gene name, 2= ordered raw pvalues). |
graph |
if TRUE a pdf graphic is created. |
method |
method for estimating m0. This must be one of the strings "adaptive", "conservative", "bootstap", "smoother" or NULL. |
lambda0 |
value used in calculating m0. |
smoothing |
"1" for the initial published method, "2" for the PAVA method isotonic (monotonely increasing nonparametric) least squares regression - see P. Broberg (2005). |
thres |
threshold defining intervals used for the movering average smoothing. |
mm |
parameter defining intervals used for the movering average smoothing. |
Value
- if graph = TRUE, a file of graphics named LocalFDRGraph.pdf
- A data file (LocalFDRFile.txt) with 4 columns : gene name, raw pvalues and two columns corresponding to smoothed FDR values.
Author(s)
J. Aubert
References
Aubert J, Bar-Hen A, Daudin J.J, Robin S (2004) Determination of the differentially expressed genes in microarrays experiments using local FDR, BMC Bioinformatics, 5:125.
Aubert J , Bar-Hen A, Daudin J.J, Robin S (2005) Correction: Determination of the differentially expressed genes in microarray experiments using local FDR, BMC Bioinformatics, 6:42.
Per Broberg (2005) A comparative review of estimates of the proportion unchanged genes and the false discovery rate, BMC Bioinformatics 6:199