[BioC] Extracting Single Channel Intensities in limma

[Sean Davis]

On Oct 1, 2004, at 8:50 AM, michael watson (IAH-C) wrote:

> You tell me, contrast matrices are a black art when it comes to
> complicated experiments.
>
> What I have are two conditions, +ve and -ve, and a control.  The design
> of the experiment is rather odd.  I have arrays that are:
>
> -ve / +ve
> -ve / +ve
> -ve / +ve
> Etc
> Etc
> -ve / Control
>
> What I want are:
>
> -ve / Control
> -ve / Control
> Etc
> +ve / Control
> +ve / Control
> Etc
>
> I figured that by using the methods decsribe in limma, I could subtract
> the single channel intensity data, and completely re-arrange the
> experiment such that all of my -ve and +ve values have the control as
> the denominator.
>
> I have no idea if this kind of complex re-arrangement can be done with 
> a
> contrast matrix.
>

Perhaps others will help us out also, but it seems to me that you have 
a common reference design, with -ve being the common reference?  If so, 
then you can refer to the limma user guide for direct guidance.  
Following the procedure for making the design matrix in the Guide, you 
will end up with a design matrix with two columns:  positive and 
Control.  The Control coefficient is Control/-ve.  The +ve coefficient 
is looking at +ve/-ve.  If you want -ve/Control and +ve/Control, you 
can specify the contrast matrix as:

makeContrasts(1-Control,positive-Control,levels=design)

This is untested, and I'm no expert, but does it give you what you want?

Sean