Hi Stanley,
Colin Smith had written this update function for reading SMD files a
little while ago. I am working towards putting them into marray at
the
moment, but you might like to try it first.
Simply
source("read.SMD2.R")
into you R dictory and try your command again.
test <- read.SMD2("5912.xls")
If there is still problems. Please e-mail the file off-line and I
will
help you with it.
Cheers
Jean
>
> I've been trying to learn R and Bioconductor and to read SMD
datasets,
> but I'm having trouble getting it to work. I can't even get it to
work
> with a small dataset (5912.xls)
>
> I'm hoping that someone can help me get past the following error:
>
> > read.SMD(fnames = NULL, path = "e:/", name.Gf = "Ch 1 Intensity
(Mean)",
> + name.Gb = "Ch 1 Background (Mean)", name.Rf = "Ch 2 Intensity
(Mean)",
> + name.Rb = "Ch 2 Background (Median)", name.W = NULL, layout =
NULL,
> + gnames = NULL, targets = NULL,notes = NULL, skip = 21, sep = " ",
> quote = "",nmax = 24192)
> [1] "Reading e://5912.xls"
> Error in readLines(con, n, ok) : invalid value for `n'
> >
>
> I just don't know where to go next to get the dataset read in. As
you
> can see, I tried to fix the number of records and should probably
fix
> the line format ('what' parameter to scan), but I suspect it should
be
> simpler than I'm making it out to be.
>
> Thanks, in advance,
> Stan
>
> --
> Stanley M Dunn, Ph.D.
> Paul S and Mary W Monroe Faculty Scholar
> Associate Dean for Graduate Education and Research
> School of Engineering
> Rutgers University
> 98 Brett Road
> Piscataway, NJ 08854
>
> (732) 445 - 4462
> (732) 445 - 3224 (Center for Packaging)
> (732) 445 - 7067 (Fax)
> smd@occlusal.rutgers.edu
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
>
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
-------------- next part --------------
read.SMD2 <- function(fnames = NULL, path = ".", name.Gf =
"CH1I_MEAN",
name.Gb = "CH1B_MEDIAN", name.Rf = "CH2I_MEAN", name.Rb =
"CH2B_MEDIAN",
name.W = NULL, layout = NULL, gnames = NULL, targets = NULL, notes
= NULL,
skip = 0, sep = "\t", quote = "", ...) {
if (is.null(fnames))
fnames <- dir(path = path, pattern = paste("*", "xls", sep =
"."))
if (is.null(path))
fullfnames <- fnames
else
fullfnames <- file.path(path, fnames)
y <- readLines(fullfnames[1], n = 100)
skip <- grepname.Gf, y)[1] - 1
smdTable <- NULL
if (is.null(layout)) {
cat("Generating layout from ", fnames[1], "\n", sep="")
smdTable <- read.table(fullfnames[1], header=TRUE, sep="\t",
quote = "", skip = skip, comment.char =
"")
numSectors <- max(smdTable$SECTOR)
xsize <- max(smdTable$X.COORD) - min(smdTable$X.COORD)
ysize <- max(smdTable$Y.COORD) - min(smdTable$Y.COORD)
maNgr <- round(sqrt(numSectors*ysize/xsize))
maNgc <- round(sqrt(numSectors*xsize/ysize))
if is.na(maNgr)) {
row <- grep("Exptid", y)[1]
exptid <- strsplit(y[row], "=")[[1]][2]
cat("Image:
http://genome-www5.stanford.edu/cgi-
bin/SMD/clickable.pl?exptid=",
exptid, "\n", sep = "")
options(warn = getOption("warn")-1)
repeat {
cat("Enter number of vertical sectors (", numSectors,
" total sectors): ", sep = "")
maNgr <- as.integer(readLines(n = 1))
if (!is.na(maNgr) && maNgr > 0 && maNgr < numSectors
&&
numSectors/maNgr == as.integer(numSectors/maNgr))
break
}
options(warn = getOption("warn")+1)
maNgc <- numSectors / maNgr
}
row <- grep("Rows per Sector", y)[1]
maNsr <- as.integer(strsplit(y[row], "=")[[1]][2])
row <- grep("Columns per Sector", y)[1]
maNsc <- as.integer(strsplit(y[row], "=")[[1]][2])
maNspots <- maNgr * maNgc * maNsr * maNsc
maSub <- rep(FALSE, maNspots)
maSub[smdTable$SPOT] <- TRUE
row <- grep("Printname", y)[1]
printname <- strsplit(y[row], "=")[[1]][2]
row <- grep("Tip Configuration", y)[1]
tipconfig <- strsplit(y[row], "=")[[1]][2]
maNotes <- paste("Print Name: ", printname,
"\nTip Configuration: ", tipconfig, sep = "")
layout <- new("marrayLayout", maNgr = maNgr, maNgc = maNgc,
maNsr = maNsr, maNsc = maNsc, maNspots =
maNspots,
maSub = maSub, maNotes = maNotes)
}
if (is.null(gnames)) {
cat("Generating probe sequence info from ", fnames[1], "\n",
sep="")
if (is.null(smdTable))
smdTable <- read.table(fullfnames[1], header=TRUE,
sep="\t",
quote = "", skip = skip,
comment.char = "")
maLabels <- as.character(smdTable$SUID)
cols <- 2:(match("SUID", colnames(smdTable))-1)
maInfo <- smdTable[,cols]
gnames <- new("marrayInfo", maLabels = maLabels, maInfo =
maInfo)
}
if (is.null(targets)) {
cat("Generating target sample info from all files\n")
maLabels <- character(0)
maInfo <- data.frame()
for (i in 1:length(fnames)) {
z <- readLines(fullfnames[i], n = skip)
row <- grep("Exptid", z)[1]
maLabels <- c(maLabels, strsplit(z[row], "=")[[1]][2])
row <- grep("Experiment Name", z)[1]
Experiment <- strsplit(z[row], "=")[[1]][2]
row <- grep("Channel 1 Description", z)[1]
Cy3 <- strsplit(z[row], "=")[[1]][2]
row <- grep("Channel 2 Description", z)[1]
Cy5 <- strsplit(z[row], "=")[[1]][2]
row <- grep("SlideName", z)[1]
SlideName <- strsplit(z[row], "=")[[1]][2]
maInfo <- rbind(maInfo, data.frame(Experiment =
Experiment,
Cy3 = Cy3, Cy5 = Cy5,
SlideName =
SlideName))
}
rownames(maInfo) <- 1:dim(maInfo)[1]
targets <- new("marrayInfo", maLabels = maLabels, maInfo =
maInfo)
}
if (is.null(notes)) {
cat("Generating notes from ", fnames[1], "\n", sep="")
row <- grep("Organism", y)[1]
organism <- strsplit(y[row], "=")[[1]][2]
row <- grep("Category", y)[1]
category <- strsplit(y[row], "=")[[1]][2]
row <- grep("Subcategory", y)[1]
subcategory <- strsplit(y[row], "=")[[1]][2]
row <- grep("Description", y)[1]
description <- strsplit(y[row], "=")[[1]][2]
row <- grep("Experimenter", y)[1]
experimenter <- strsplit(y[row], "=")[[1]][2]
row <- grep("Contact email", y)[1]
email <- strsplit(y[row], "=")[[1]][2]
row <- grep("Scanning Software", y)[1]
software <- strsplit(y[row], "=")[[1]][2]
row <- grep("Software version", y)[1]
version <- strsplit(y[row], "=")[[1]][2]
row <- grep("Scanning parameters", y)[1]
parameters <- strsplit(y[row], "=")[[1]]
if (length(parameters) > 1)
parameters <- paste(parameters[2:length(parameters)],
collapse = ", ")
else
parameters <- NA
notes <- paste("Organism: ", organism,
"\nCategory: ", category,
"\nSubcategory: ", subcategory,
"\nDescription: ", description,
"\nExperimenter: ", experimenter,
"\nE-Mail: ", email,
"\nScanning Software: ", software, " ",
version,
"\nScanning Parameters: ", parameters, sep =
"")
}
mraw <- read.marrayRaw(fnames = fnames, path = path, name.Gf =
name.Gf,
name.Gb = name.Gb, name.Rf = name.Rf, name.Rb = name.Rb,
name.W = name.W, layout = layout, gnames = gnames, targets =
targets,
notes = notes, skip = skip, sep = sep, quote = quote,
...)
return(mraw)
}
