Create objects of class "marrayRaw"
This function reads in cDNA microarray data from a directory and creates objects of
class "marrayRaw" from spot quantification data files obtained from image analysis software or databases.
read.marrayRaw(fnames, path=".", name.Gf=NULL, name.Gb=NULL, name.Rf=NULL,
name.Rb=NULL,name.W=NULL, layout=NULL, gnames=NULL, targets=NULL,
notes=NULL, skip=NULL, sep=" ", quote="\"", DEBUG=FALSE, ...)
read.GenePix(fnames = NULL, path = NULL, name.Gf = "F532 Median",
name.Gb ="B532 Median", name.Rf = "F635 Median", name.Rb = "B635 Median",
name.W ="Flags", layout = NULL, gnames = NULL, targets = NULL,
notes = NULL, skip=NULL, sep = " ", quote = "\"", DEBUG=FALSE, ...)
read.SMD(fnames = NULL, path = NULL, name.Gf = "Ch1 Intensity (Median)",
name.Gb = "Ch1 Background (Median)", name.Rf = "Ch2 Intensity (Median)",
name.Rb = "Ch2 Background (Median)", name.W = NULL, info.id = c("Name",
"Clone ID"), layout = NULL, gnames = NULL, targets = NULL, notes = NULL, skip = NULL, sep = "\t", quote = "\"", DEBUG=FALSE, ...)
read.Spot(fnames = NULL, path = ".", name.Gf = "Gmean", name.Gb =
"morphG", name.Rf = "Rmean", name.Rb = "morphR",name.W = NULL, layout =
NULL, gnames = NULL, targets = NULL, notes = NULL, skip = NULL, sep = "\t", quote = "\"", DEBUG=FALSE, ...)
read.Agilent(fnames = NULL, path=NULL, name.Gf = "gMedianSignal", name.Gb = "gBGMedianSignal", name.Rf = "rMedianSignal", name.Rb = "rBGMedianSignal", name.W= NULL, layout = NULL, gnames = NULL, targets = NULL, notes=NULL, skip=NULL, sep="\t", quote="\"", DEBUG=FALSE, info.id=NULL, ...)
widget.marrayRaw(ext = c("spot", "xls", "gpr"), skip = 0, sep = "\t", quote = "\"", ...)fnames |
a vector of character strings containing the file names of
each spot quantification data file. These typically end in |
path |
a character string representing the data directory. By
default this is set to the current working directory ("."). In the
case where |
name.Gf |
character string for the column header for green foreground intensities. |
name.Gb |
character string for the column header for green background intensities. |
name.Rf |
character string for the column header for red foreground intensities. |
name.Rb |
character string for the column header for red background intensities. |
name.W |
character string for the column header for spot quality weights. |
layout |
object of class |
gnames |
object of class |
targets |
object of class |
notes |
object of class |
info.id |
object of class |
skip |
the number of lines of the data file to skip before beginning to read in data. |
sep |
the field separator character. Values on each line of the file are separated by this character. The default is to read a tab delimited file. |
quote |
the set of quoting characters. By default, this is
disabled by setting |
ext |
a characters string representing suffix of different image analysis output files. |
DEBUG |
a logical value, if TRUE, a series of echo statements will be printed. |
... |
further arguments to |
An object of class "marrayRaw".
Jean Yang, yeehwa@stat.berkeley.edu
datadir <- system.file("swirldata", package="marray")
## Quick guide
swirl.targets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt"))
data <- read.Spot(path=datadir, targets=swirl.targets)
## Alternate commands
skip <- grep("Row", readLines(file.path(datadir,"fish.gal"), n=100)) - 1
swirl.layout <- read.marrayLayout(ngr=4, ngc=4, nsr=22, nsc=24)
swirl.targets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt"))
swirl.gnames <- read.marrayInfo(file.path(datadir, "fish.gal"),
info.id=4:5, labels=5, skip=skip)
x <- maInfo(swirl.gnames)[,1]
y <- rep(0, maNspots(swirl.layout))
y[x == "control"] <- 1
slot(swirl.layout, "maControls") <- as.factor(y)
fnames <- dir(path=datadir,pattern="spot")
swirl<- read.Spot(fnames, path=datadir,
layout = swirl.layout,
gnames = swirl.gnames,
targets = swirl.targets)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.