[BioC] Using limma with Applied Precision SoftWorx data

[David Henderson]

Hi Susan:

> Does anyone have experience using limma with 2-color microarray data 
> obtained from the Applied Precision SoftWorx Tracker?  I can read the 
> .txt files with read.maimages but I don't know how to create a Layout 
> for normalizeWithinArrays.  It seems that I should be able to map the 
> Set/Set Row/Set Column values to Block/Row/Columns but I am not sure 
> about this.  Any help would be much appreciated.

So, Nirav purchased some cheap array scanner software for you to
use? ;^)

Just kidding...  You should be able to create a layout for this object
by creating a list with the following elements (note grid and block are
interchangeable):

ngrid.r <- # grid rows
ngrid.c <- # grid columns
nspot.r <- # rows within each grid
nspot.c <- # columns within each grid
ndups <- # duplicate spots
spacing <- # spots between duplicate spots
npins <- # print pins in the print head that printed the array
start <- the starting point for printing each grid, i.e. "topleft" or
"topright"

Then, set rg$printer <- yourlist where yourlist is the list you created
using the above map and rg is your RGList object.

Good Luck!!

Dave H
-- 
David A. Henderson, Ph.D.
Insightful Corporation
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