plgem.deg {plgem}R Documentation

Selection of Differentially Expressed Genes using PLGEM

Description

This function compares observed PLGEM-derived STN statistics with resampled test statistics, and selects the differentially expressed genes (DEG) with a given significance level ‘delta’.

Usage

plgem.deg(observedStn, plgemResampledStn, delta = 0.001, verbose = FALSE)

Arguments

observedStn matrix of observed signal to noise ratios (STN); output of function ‘plgem.obsStn’.
plgemResampledStn list; the output of function ‘plgem.resampledStn’.
delta number or array; the significance level(s) used for the DEG selection, value(s) must be in (0,1).
verbose logical; if TRUE, comments are printed out while running.

Details

This function allows for the selection of DEG by comparing their observed and resampled STN. ‘delta’ roughly represents the false positive rate of the DEG selection, e.g. if a ‘delta’ of 0.001 is chosen in a microarray with 10000 entries, 10 of the selected DEG are expected to be false positives.

Value

This function returns a list with a number of items is equal to the number of different significance levels (‘delta’) used as input. Each item is again a list, whose number of items correspond to the number of performed comparisons, i.e. the number of conditions in the starting exprSet minus the baseline. In each list-item the values are the observed STN and the names are the DEG probeset ids.

Author(s)

Mattia Pelizzola mattia.pelizzola@unimib.it and Norman Pavelka norman.pavelka@unimib.it

References

N. Pavelka et al., BMC Bioinformatics, 2004 Dec 17;5(1):203; http://www.genopolis.it

See Also

plgem.fit,plgem.obsStn,plgem.resampledStn,run.plgem

Examples

data(LPSeset)
LPSfit<-plgem.fit(data = LPSeset, fittingEval = TRUE)
LPSobsStn<-plgem.obsStn(data = LPSeset, plgemFit = LPSfit)
LPSresampledStn<-plgem.resampledStn(data = LPSeset, plgemFit = LPSfit)
LPSdegList<-plgem.deg(observedStn = LPSobsStn, plgemResampledStn = LPSresampledStn, delta = 0.001)

[Package plgem version 1.6.0 Index]