affystart: Pre-processing for Affymetrix Data

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

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,
  output = "txt",
  annotate = FALSE,
  ann.vec = c("SYMBOL", "GENENAME", "ENTREZID", "UNIGENE", "REFSEQ")
)

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.
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.

Value

Returns an ExpressionSet.

Author(s)

James W. MacDonald <[e-mail]>

See Also

plotHist, plotDeg, plotPCA

jmacdon/affycoretools documentation built on Nov. 2, 2024, 1:29 a.m.