[BioC] agi4x44kpreprocess: `GEhelp` and `Treatment` variables

James W. MacDonald jmacdon at uw.edu
Wed Nov 13 22:24:15 CET 2013

Hi Stephen,

On Wednesday, November 13, 2013 2:16:50 PM, Stephen Hwang wrote:
> I recently came across your R package `Agi4x44PreProcess` and I'm having
> issues with the filtering step due to my `targets` file (I did not include
> a `Treatment` or a GErep` column).
>                 Cy3              Cy5
> Array1:  pre-drug    pre-drug
> Array2:  pre-drug    post-drug
> Array3:  post-drug  pre-drug
> How would I label these groups? If treatment groups are 'pre-pre',
> 'pre-post', and 'post-pre', are the GErep values would be `1`, `2`, and
> `3`, corresponding to each treatment group?

The Agi4x44PreProcess package is designed for Agilent 4x44 arrays, 
which if I am not mistaken are all single channel arrays. It appears 
you are not using that type of array, so you would likely be better 
served by using the limma package directly.

There are numerous examples in the limma User's Guide that show how to 
analyze two channel arrays:




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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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