Description Usage Arguments Details Value Note Author(s) References See Also Examples
Performs bayesian t tests on a gene expression matrix.
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x 
A 
y 
If 
type 

m 
Size of the sliding window that is used obtain the background variance from pooled similarly expressed genes, s. details. 
conf 
The number of 'pseudocounts' giving weight to the prior variance, s. details. 
pvalues 
Should pvalues be computed ? Default is 
gene.names 
An optional vector of gene names. 
... 
Currently unused argument. 
The argument m
determines the width of the window
used to obtain an estimate for the average variability of
gene expression for those genes that show a similar expression level.
The argument conf
is nonnegative and denotes the weight given to the Bayesian prior estimate of withintreatment
variance. Baldi and Long report reasonable performance with this parameter set equal to approximately 3 times the number of
observations, when the number of experimental observations is small (approximately 4 or less).
If the number of replicate experimental observations is large then the confidence value can be lowered
to be equal to the number of observations (or even less).
An object of class GeneRanking.
Results can differ slightly from the CyberTSoftware of Baldi and Long.
Martin Slawski
AnneLaure Boulesteix
Baldi,P., Long, A.D. (2001).
A Bayesian framework for the analysis of microarray data.
Bioinformatics, 17, 509519
RepeatRanking, RankingTstat, RankingFC, RankingWelchT, RankingWilcoxon, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation
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