 Good evening, Prof. Jean Yee Hwa Yang.

I've heard of you a lot. Thank you very much for your advice.

My project is to complete the print-tip normalization. After I normalize the
data with "maNorm", I still get 48 loess lines.
As far as I know, when we make microarray chips, we use only 16 tips and use
it three times for 48 grids. I mean that 3 different blocks out of 48 blocks
are printed by same print-tip. So, we need only 16 loess line for each tips.
However, as we can see with ">bcGAL$layout ", maNgr (the number of rows for
the grid matrix) is 12 and maNgc(the number of columns for the grid
matrix) is 4. Does that mean we have 48 print-tips and I don't have to do
further normalization? I am really curious.

Best regards,
Joo Sang Lee

On 10/4/06, Jean Yee Hwa Yang <jeany@maths.usyd.edu.au> wrote:
>
> 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@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>

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