sva.check: A function for post-hoc checking of an sva object to check...
In sva: Surrogate Variable Analysis

Description Usage Arguments Details Value Examples

This function is designed to check for degenerate cases in the sva fit and fix the sva object where possible.

1	sva.check(svaobj, dat, mod, mod0)

`svaobj`	The transformed data matrix with the variables in rows and samples in columns
`dat`	The data set that was used to build the surrogate variables
`mod`	The model matrix being used to fit the data
`mod0`	The null model matrix being used to fit the data

empirical.controls for a direct estimate of the empirical controls.

sv The estimated surrogate variables, one in each column

pprob.gam: A vector of the posterior probabilities each gene is affected by heterogeneity

pprob.b A vector of the posterior probabilities each gene is affected by mod

n.sv The number of significant surrogate variables

library(bladderbatch)
data(bladderdata)
#dat <- bladderEset
dat <- bladderEset[1:5000,]

pheno = pData(dat)
edata = exprs(dat)
mod = model.matrix(~as.factor(cancer), data=pheno)
mod0 = model.matrix(~1,data=pheno)

n.sv = num.sv(edata,mod,method="leek")
svobj = sva(edata,mod,mod0,n.sv=n.sv)
svacheckobj = sva.check(svobj,edata,mod,mod0)