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) [[alternate HTML version deleted]]

Hi Barry, If you specify your layout and the data seprately. The marray packages do assume you are reading your data file in certain order. But it looks like you are reading a typical Gal file. If you are reading a gal file from GenePix, could you try the following and gal <- read.Galfile("gene.txt", info.id=1:6) ## this way, all row and col information are store. object <- gal$layout Gnames <- gal$gnames tmp <- data.frame(GR = maGridRow(object), GC = maGridCol(object), SR = maSpotRow(object), SC = maSpotCol(object), maInfo(Gnames)) tmp[1:10,] ## Check that the output is the same as your input Alternative, if you send me a small samples, I am happy to try it out to determine if it's a bug in our package. Cheers Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Division of Biostatistics, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Fri, 14 Mar 2003, Barry Henderson wrote: > 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) > > > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >