[BioC] Spot matrix manglings?
Barry Henderson
barry.henderson at ribonomics.com
Fri Mar 14 17:36:39 MET 2003
I have noticed that BioC is not maintaining the original spot matrix
coordinates in my original data files (I'm accessing the coordinates via
maSpotRow and maSpotCol). Reading the vignettes I see that the
marrayLayout Class "computes" layout parameters. Is it normal behavior
for the marrayLayout methods to reorder spot coordinates within a
subgrid???? Or am making an error in reading the data into BioC,
spitting the coordinates out?
I'm concerned since I was was going to export the data compiled from a
large set of individual data files using BioC into an ordered file for
analysis elsewhere. As I will be doing spatial normalization I am
concerned about this reordering. It appears as though it should not be
a problem since I the ordering appears to be occurring only within
subgrids.
An example of the input and output matrices are pasted below as well as
the code used to read the data into BioC.
thanks in advance
Barry
Starting Grid Location BioC Computed
Grid locations
MetaRow MetaColumn Row Column GeneID MR MC
Row Col GeneID
1 1 1 1 AF191028 1 1
1 1 AF191028
1 1 1 2 AF247559 1 1
1 2 X56062
1 1 1 3 AF168390 1 1
1 3 NM_015453
1 1 1 4 X14212 1 1 1
4 NM_007204
1 1 1 5 U91966 1 1 1
5 XM_031044
1 1 1 6 X58149 1 1 1
6 NM_005481
1 1 1 7 AF198054 1 1
1 7 AF247559
1 1 1 8 AF159803 1 1
1 8 AF168390
1 1 1 9 AF159801 1 1
1 9 X14212
1 1 1 10 X56062 1 1 1
10 U91966
1 1 1 11 NM_015453 1 1 1
11 X58149
1 1 1 12 NM_007204 1 1 1
12 AF198054
1 1 1 13 XM_031044 1 1 1
13 AF159803
1 1 1 14 NM_005481 1 1 1
14 AF159801
exp.layout <- read.marrayLayout(fname=file.path(datadir, "genes.txt"),
ngr= 4, ngc = 4, nsr = 12, nsc = 14, skip=0, ctl.col= 6)
ctl <- rep("Control", maNspots(exp.layout))
ctl[maControls(exp.layout) != "Control"] <- "normal"
maControls(exp.layout) <- factor(ctl)
#Load Sample data from samples.txt
exp.samples <- read.marrayInfo(file.path(datadir, "samples.txt"))
#Load gene names from gal file
exp.gnames <- read.marrayInfo(file.path(datadir, "genes.txt"), info.id =
5:6, labels = 5, skip = 0)
# Read data files....
fnames <- dir(path = datadir, pattern = paste("*", "Rinput", sep = "."))
exp.raw <- read.marrayRaw(fnames, path = datadir, name.Gf = "GreenSig",
name.Gb = "GreenBkg", name.Rf = "RedSig", name.Rb = "RedBkg", layout =
exp.layout, gnames = exp.gnames, targets = exp.samples)
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