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
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.