[BioC] marrayInput: different gal files for the same experiment

Jean Yee Hwa Yang jean at biostat.ucsf.edu
Mon Apr 5 19:30:55 CEST 2004

Hi Scott,

Every marrayraw object will only stores array from one print-run because
we also specify the array layout information.  I normalized within each
print-run seprately and than combined the log-ratios.  This will work
nicely for most arrays.  However, if you have duplicates spots for all
probes, you will need to use functions in Limma to combined the


 Jean Yee Hwa Yang			 jean at biostat.ucsf.edu
 Lung Biology Center, 		           Tel: (415) 476-3368
 University of California,		   Fax: (415) 476-6014
 500 Parnassus Avenue, MU 420-W,  San Francisco, CA 94143-0560

On Fri, 2 Apr 2004, Scott Rifkin wrote:

> I have experiment with lots of arrays which are from a few different
> printings.  In one of the printings, one plate was printed out of order.  
> In another, the layout is slightly different from the rest (and is missing
> a few spots the others have).  Consequently, I have three different gal
> files.  I would like to analyze all the arrays together (to do some
> between slide normalization) and so would like to read them into the same
> marray object.  It isn't clear to me how to do this.
> thanks,
> Scott Rifkin
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