plgem.deg {plgem} | R Documentation |
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’.
plgem.deg(observedStn, plgemResampledStn, delta = 0.001, verbose = FALSE)
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. |
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.
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.
Mattia Pelizzola mattia.pelizzola@unimib.it and Norman Pavelka norman.pavelka@unimib.it
N. Pavelka et al., BMC Bioinformatics, 2004 Dec 17;5(1):203; http://www.genopolis.it
plgem.fit
,plgem.obsStn
,plgem.resampledStn
,run.plgem
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)