RankingBaldiLong {GeneSelector} | R Documentation |
Performs bayesian t tests on a gene expression matrix.
For S4
method information, see RankingBaldiLong-methods.
RankingBaldiLong(x, y, type = c("unpaired", "paired", "onesample"), m = 100, conf = NULL, pvalues = TRUE, gene.names = NULL, ...)
x |
A matrix of gene expression values with rows
corresponding to genes and columns corresponding to observations or alternatively an object of class ExpressionSet .If type = paired , the first half of the columns corresponds to
the first measurements and the second half to the second ones.
For instance, if there are 10 observations, each measured twice,
stored in an expression matrix expr ,
then expr[,1] is paired with expr[,11] , expr[,2]
with expr[,12] , and so on. |
y |
If x is a matrix, then y may be
a numeric vector or a factor with at most two levels.If x is an ExpressionSet , then y
is a character specifying the phenotype variable in
the output from pData .If type = paired , take care that the coding is
analogously to the requirement concerning x |
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 p-values be computed ? Default is TRUE . |
gene.names |
An optional vector of gene names. |
... |
Currently unused argument. |
The argument m
determines the width of the window
used to provides an estimate of the average variability of
gene expression for those genes that show a similar expression level.
The argument conf
is non-negative and indicates the weight give to the Bayesian prior estimate of within-treatment
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 slighlty from the Cyber-T-Software of Baldi and Long.
Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix
Baldi,P., Long, A.D. (2001).
A bayesian framework for the analysis of microarray data.
Bioinformatics, 17, 509-519
GetRepeatRanking, RankingTstat, RankingFC, RankingWelchT, RankingWilcoxon, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingBstat, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation, RankingGap
## Load toy gene expression data data(toydata) ### class labels yy <- toydata[1,] ### gene expression xx <- toydata[-1,] ### run RankingBaldiLong BaldiLong <- RankingBaldiLong(xx, yy, type="unpaired")