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

[Jean Yee Hwa Yang]

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
print-runs.

Cheers

Jean
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 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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