Description Usage Arguments Value Author(s) References See Also Examples
Uses the methods of fitGAPLM
to generate linear models of the class
MArrayLM
so that the moderated t and F methods of limma
may be used to test for differential gene expression. See fitGAPLM
for more a more in-depth description of the inputs.
1 2 3 4 5 6 7 | limmaPLM(dataObject, intercept = TRUE,
indicators = as.character(unique(dataObject$sampleInfo[,2])[-1]),
continuousCovariates = NULL,
groups = as.character(unique(dataObject$sampleInfo[,2])[-1]),
groupFunctions = rep("AdditiveSpline", length(groups)),
fitSplineFromData = TRUE, splineDegrees = rep(3, length(groups)),
splineKnots = rep(0, length(groups)), splineKnotSpread = "quantile", ...)
|
dataObject |
An object of type |
intercept |
Should an intercept term be included in the model? |
indicators |
Same as |
continuousCovariates |
Same as |
groups |
Same as |
groupFunctions |
Same as |
fitSplineFromData |
Same as |
splineDegrees |
Same as |
splineKnots |
Same as |
splineKnotSpread |
Same as |
... |
parameters to be passed to |
This method returns an MarrayLM
object on which we can call eBayes()
and topTable()
to test for differentially expressed genes.
Jonas Mueller
Smyth, G. K. Linear Models and empirical Bayes methods for assesing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 3, Article 3 (2004).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ## create an object of type \code{plmDE} containing disease
## with "control" and "disease" and measurements of weight and severity:
ExpressionData = as.data.frame(matrix(abs(rnorm(10000, 1, 1.5)), ncol = 100))
names(ExpressionData) = sapply(1:100, function(x) paste("Sample", x))
Genes = sapply(1:100, function(x) paste("Gene", x))
DataInfo = data.frame(sample = names(ExpressionData), group = c(rep("Control", 50),
rep("Diseased", 50)), weight = abs(rnorm(100, 50, 20)), severity = c(rep(0, 50),
abs(rnorm(50, 100, 20))))
plmDEobject = plmDEmodel(Genes, ExpressionData, DataInfo)
## create a linear model from which various hypotheses can be tested:
toTest = limmaPLM(plmDEobject, continuousCovariates = c("weight", "severity"),
fitSplineFromData = TRUE, splineDegrees = rep(3, length(groups)),
splineKnots = rep(0, length(groups)), splineKnotSpread = "quantile")
## view the coefficients/variables in the model:
toTest$coefficients[1, ]
weightCoefficients = c("DiseasedBasisFunction.weight.1",
"DiseasedBasisFunction.weight.2", "DiseasedBasisFunction.weight.3",
"DiseasedBasisFunction.weight.4", "DiseasedBasisFunction.weight.5",
"DiseasedBasisFunction.weight.6", "DiseasedBasisFunction.weight.7",
"DiseasedBasisFunction.weight.8", "DiseasedBasisFunction.weight.9")
## test the significance of weight in variation of the expression levels:
toTestCoefficients = contrasts.fit(toTest, coefficients = weightCoefficients)
moderatedTest = eBayes(toTestCoefficients)
topTableF(moderatedTest)
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