affystart {affycoretools} | R Documentation |
This function is designed to automatically read in all cel files in a directory, make all pre-processing QC plots and compute expression measures.
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"))
... |
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. |
Returns an exprSet
.
James W. MacDonald <jmacdon@med.umich.edu>
plotHist
, plotDeg
, plotPCA