Pre-processing for Affymetrix Data

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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

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affystart(..., filenames = NULL, groups = NULL, groupnames = NULL,
  plot = TRUE, pca = TRUE, squarepca = FALSE, plottype = "pdf",
  express = c("rma", "mas5", "gcrma"), addname = NULL, output = "txt",
  annotate = FALSE, ann.vec = c("SYMBOL", "GENENAME", "ENTREZID", "UNIGENE",
  "REFSEQ"))

Arguments

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.

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.

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.

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).

output

What format to use for the output of expression values. Currently only supports text format.

annotate

Boolean. Add annotation data to the output file?

ann.vec

A character vector of annotation data to add to the output file.

...

Requires that all variables be named.

Value

Returns an ExpressionSet.

Author(s)

James W. MacDonald <jmacdon@u.washington.edu>

See Also

plotHist, plotDeg, plotPCA

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