Hello. I just started studying bioinformatics. I have trouble in using marray package. I am using smd data including excel files and bc.gal file. My code is as follows. ---------------------------------------------------------------------- ----------- library(marray) datadir("~/smd") bcGAL<-read.Galfile("bc.gal",path=datadir) fnames<-dir(path=datadir,pattern=".xls") bc<-read.marrayRaw(fnames,path=datadir,name.Gf="Ch1 Inetnsity (Mean)", name.Gb="Ch1 Background (Median)", name.Rf="Ch2 Intensity (Mean)" naem.Rb="Ch2 Background (Median)",name.W="Spot Flag",sep="\t",skip=0,layout=bcGAL$layout,gnames=bcGAL$gnames) plot(bc) ---------------------------------------------------------------------- ----------- The result plot has not 4 by 4 but 12 by 4 loess lines. I have no idea how to fix this problem. Please give me some advice. Any help or comment would be appreciated.

Hi, Whether it is 4 by 4 or 12 by 4 depends on the layout of your array. So if you have 48 grids on the array, it generally will be 12 by 4 (48) loess lines. The swirl example happends to be an array with 4 by 4 grids and hence you see (4 by 4) 16 lines. Have a look at the > bcGAL$layout Cheers Jean > library(marray) > datadir("~/smd") > bcGAL<-read.Galfile("bc.gal",path=datadir) > fnames<-dir(path=datadir,pattern=".xls") > > bc<-read.marrayRaw(fnames,path=datadir,name.Gf="Ch1 Inetnsity (Mean)", > name.Gb="Ch1 Background (Median)", name.Rf="Ch2 Intensity (Mean)" naem.Rb="Ch2 > Background (Median)",name.W="Spot > Flag",sep="\t",skip=0,layout=bcGAL$layout,gnames=bcGAL$gnames) > > plot(bc) > -------------------------------------------------------------------- ------------- > > The result plot has not 4 by 4 but 12 by 4 loess lines. I have no idea how to > fix this problem. > > Please give me some advice. Any help or comment would be appreciated. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >