snm (version 1.20.0)

snm.fitted: Extract fitted values from an snm object

Description

Computes fitted values under models used in snm normalization.

Usage

snm.fitted(object, ...)
"fitted"(object, ...)

Arguments

object

Output from the snm function.

...

Not used.

Value

fit0

Linear model fits when regressing each probe's normalized data on the null model, ~adj.var.

fit1

Linear model fits when regressing each probe's normalized data on the full model, ~adj.var+bio.var.

Details

Returns the fitted values under the "null model" (adjustment variables only) and the "full model" (adjustment variables + biological variables).

References

Mecham BH, Nelson PS, Storey JD (2010) Supervised normalization of microarrays. Bioinformatics, 26: 1308-1315.

See Also

snm, sim.singleChannel

Examples

## Not run: 
# singleChannel <- sim.singleChannel(12345)
# snm.obj <- snm(singleChannel$raw.data,
# 		      singleChannel$bio.var,
# 		      singleChannel$adj.var[,-6],
# 		      singleChannel$int.var, num.iter=10)
# snm.fit = fitted(snm.obj)
# res1 = snm.obj$norm.dat - snm.fit$fit1
# snm.svd = fast.svd(res1)
# cor(snm.svd$v[,1], singleChannel$adj.var[,6])
# plot(snm.svd$v[,1], singleChannel$adj.var[,6])
# ## End(Not run)