[BioC] Having trouble in using marray

[Jean Yee Hwa Yang]

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.
>
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