affystart {affycoretools}R Documentation

Pre-processing for Affymetrix Data

Description

This function is designed to automatically read in all cel files in a directory, make all pre-processing QC plots and compute expression measures.

Usage

affystart(..., filenames=NULL, groups = NULL, groupnames = NULL, plot =
TRUE, pca = TRUE,  squarepca = FALSE, plottype="pdf", express = c("rma",
"mas5", "gcrma"), addname = NULL, phenoData = new("phenoData"))

Arguments

... Requires that all variables be named
filenames If not all cel files in a directory will be used, pass a vector of filenames.
groups An integer vector indicating the group assignments for the PCA plot.
groupnames A character vector with group names for PCA legend.
plottype What type of plot to save. Can be "pdf","postscript", "png","jpeg", or "bmp". Defaults to "pdf". Note that "png" and "jpeg" may not be available on a given computer. See the help page for capabilities and png for more information.
plot Should density and degradation plots be made? Defaults to TRUE.
pca Should a PCA plot be made? Defaults to TRUE.
squarepca Should the y-axis of the PCA plot be made comparable to the x-axis? This may aid in interpretation of the PCA plot. Defaults to FALSE
express One of either rma, mas5, gcrma. Defaults to rma. Partial matching OK.
addname Used to append something to the name of the pca plot and the expression values output file (e.g., if function is run twice using different methods to compute expression values)
phenoData A phenoData object.

Value

Returns an exprSet.

Author(s)

James W. MacDonald <jmacdon@med.umich.edu>

See Also

plotHist, plotDeg, plotPCA


[Package affycoretools version 1.8.1 Index]