getResidPerGene {GSEAlm} | R Documentation |
This produces residuals of an identical linear model applied to each row of a gene expression matrix (or similar dataset). Computation speed is achieved via straightforward matrix algebra. Most commonly-used residual types are available.
getResidPerGene(lmobj, type = "extStudent")
lmobj |
An object produced by function lmPerGene . |
type |
A string indicating the type of residual requeseted (defaults to externally-Studentized). |
Types of residuals now available:
Returns a instance of ExpressionSet
where the expression matrix
contains the residuals. The phenoData
are inherited from
lmobj$eS
.
Robert Gentleman, Assaf Oron
lmPerGene
, resplot
,dfbetasPerGene
,influence.measures
data(sample.ExpressionSet) lm1 = lmPerGene(sample.ExpressionSet,~sex) r1 = getResidPerGene(lm1) ### now a boxplot of all residuals by sample resplot(resmat=exprs(r1),fac=sample.ExpressionSet$sex) ### This plot is not very informative because of some gross outliers; ### try this instead resplot(resmat=exprs(r1),fac=sample.ExpressionSet$sex,lims=c(-5,5))