marrayTools {marray}R Documentation

Wrapper function

Description

This functions will produce a directory of diagnostic plots, quality measures and normalization.

Usage

spotTools(fnames, path = ".", galfile, bg = TRUE, plot = TRUE,
                 quality = TRUE, fill = TURE, raw = FALSE, echo =
                 TRUE, ...)

gpTools(fnames, path = ".", galfile, bg = TRUE, plot = TRUE, quality = TRUE, fill = TRUE, raw = FALSE, echo = TRUE, ...)

Arguments

fnames a vector of character strings containing the file names of each spot quantification data file. These typically end in .spot for the software Spot or .gpr for the software GenePix.
path a character string representing the data directory. By default this is set to the current working directory ("."). In the case where fnames contains the full path name, path should be set to NULL.
galfile a character string representing the Gal file.
bg logical: if 'TRUE', background correction is performed before normalization
plot logical: if 'TRUE', maDiagnPlots is call to generate basic diagnostic plot per array.
quality logical: if 'TRUE', maQuality is call to calculate basic quality measures.
fill logical: if `TRUE', `scan' will implicitly add empty fields to any lines with fewer fields than implied by `what'.
raw logical: if 'TRUE', the microarray object class of 'marrayRaw' is return rather than 'marrayNorm'.
echo logical: if 'TRUE' (default), run-time information of the array currently being process is printed.
... further arguments to scan or maNorm.

Value

Jpeg files of diagnostic plots, excel files of quality measures, tab delimited files of normalized log-ratios and log-intensities values are saved to disk. In addition, an object of class marrayRaw or marrayNorm is return.

Author(s)

Yee Hwa (Jean) Yang

See Also

read.marrayRaw

Examples

 data(swirl)
 datadir <- system.file("swirldata", package="marray")

## normdata <- spotTools(path=datadir, quality=FALSE)

[Package marray version 1.5.14 Index]