[BioC] Spot matrix manglings?

[Barry Henderson]

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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