plgem.obsStn {plgem} | R Documentation |
These functions compute the observed and resampled signal to noise ratio (STN) statistic using PLGEM fitting parameters (obtained using the function ‘plgem.fit’) to detect differential expression in a microarray exprSet ‘data’.
plgem.obsStn(data, plgemFit, baseline.condition = 1, verbose = FALSE) plgem.resampledStn(data, plgemFit, baseline.condition = 1, iterations = "automatic", verbose=FALSE)
data |
an object of class ‘exprSet’ with a ‘conditionName’ covariate, see details. |
plgemFit |
list; the output of ‘plgem.fit’. |
baseline.condition |
the condition to be treated as the baseline. |
verbose |
logical; if TRUE, comments are printed out while running. |
iterations |
number of iterations for the resampling step; if "automatic" it is automatically determined. |
The exprSet ‘data’ must have at least two conditions; by default the first one is considered the baseline. ‘data’ must have a phenoData slot with a covariate called ‘conditionName’. The values of this covariate must be sample labels, that have to be identical for samples to be treated as replicates.
PLGEM-STN statistic determines the degree of differential expression between a condition and the baseline:
PLGEM-STN = [mean(condition)-mean(baseline)] / [modeledSpread(condition)+modeledSpread(baseline)],
where: ln(modeledSpread) = PLGEMslope * ln(mean) + PLGEMintercept
‘plgem.obsStn’ determines the observed PLGEM-STN values for each probeset of ‘data’. ‘plgem.resampledStn’ determines the resampled PLGEM-STN values for each probeset of ‘data’ using a resampling approach; see References for details. The number of iterations should be correlated with the number of replicates of the condition used for model fitting.
‘plgem.obsStn’ returns a matrix of observed PLGEM-STN. The rownames of the matrix are the ‘data’ probeset ids.
‘plgem.resampledStn’ returns a list with two items:
RESAMPLED.STN |
matrix of resampled PLGEM-STN whose rownames of the matrix are the ‘data’ probeset ids, and the columns represent the different replication schema of the provided comparisons; see References for details. |
REPL.NUMBER |
the number of replicates found for each experimental condition; see References for details. |
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
data(LPSeset) LPSfit<-plgem.fit(data = LPSeset, fittingEval = TRUE) LPSobsStn<-plgem.obsStn(data = LPSeset, plgemFit = LPSfit) LPSresampledStn<-plgem.resampledStn(data = LPSeset, plgemFit = LPSfit)