arrayQuality (version 1.50.0)

PRv9mers: Print Run Quality version 9mers

Description

Qualitative diagnostic plots looking at print-run quality. This component examine the 9mers hybridizations.

Usage

PRv9mers(fnames, path = ".", dev = "png", DEBUG = FALSE, prargs = NULL, samepr = TRUE, prname = "xMm", save = TRUE, ...)

Arguments

fnames

A "character" string naming the input files.

path

A "character" string representing the data directory. By default this is set to the current working directory (".").

dev

A "character" string naming the graphics device. This will take arguments "png", "jpeg" and "ps" only.

DEBUG

If 'TRUE', debug statements are printed.

prargs

A list with 4 components: Block, Row, Column and ncolumns. See Details for more information.

samepr

If 'TRUE', we assume everything in the directory are from the same print-run.

prname

A "character" string giving the name of the print-run.

save

If `TRUE', the figures will be saved to files.

...

additional arguments

Value

Files of diagnostic plots and excel files containings probe IDs of problematic probes.

Details

The argument "prargs" is used to calculate the layout information about a print-run. Components Block, Row and Columns denote the column names from the input data representing the print-tip location. The component "ncolumns" is an integer representing the number of print-tip columns in the data. If the argument is set to NULL, the the following default will be used: list(Block="Block", Row="Row", Column="Column", ncolumns=4).

Examples

datadir <- system.file("gprQCData", package="arrayQuality")
if (interactive())
PRv9mers(fnames="12Mm250.gpr", path=datadir, prname="12Mm")