compute.RA {FLUSH.LVS.bundle} | R Documentation |
Given an AffyBatch
object fits a robust linear model at probe level and return the residual standard errors and the array effects.
compute.RA(abatch,bg.RA=c("nome","imm","rma"))
an object of class RA with a 'data' slot containing a two columns data.frame with IDs as rows and RSE and Array effects as columns.
Stefano Calza <calza@med.unibs.it>, Davide Valentini and Yudi Pawitan.
S. Calza et al. 'Normalization of oligonucleotide arrays based on the least variant set of genes' (2008, BMCBioinformatics).
lvs
, normalize.lvs
, lvs.fit
, normalize.AffyBatch.lvs
fitRA
## Not run: # Starting from an Affibatch object called aBatch data.RA <- compute.RA(aBatch) lvs.id <- lvs.fit(data.RA, proportion=0.6) lvs.prep <- expresso(aBatch, normalize=FALSE, bgcorrect.method="mas",pmcorrect.method="mas",summary.method="mas") normalize.AffyBatch.lvs(lvs.prep,lvs.id=lvs.id) ## End(Not run)