[BioC] two color arrays normalization

[Naomi Altman]

This will make no difference to the statistical tests and 
p-values.  The simplest ways to get the M values right are:

Either: Create the design matrix as in the limma manual - say 
designMatrix. Then switch sign.

designMatrix= - designMatrix

Then proceed as in the manual.

Or: Create the design matrix and do the analysis (without switching 
sign).  Call the output fit.out.
The M-values are in fit.out$coef.

fit.out$coef= - fit.out$coef






At 10:32 PM 2/9/2009, Giusy Della Gatta wrote:
>Hi Naomi,
>my colleague told me that in the calculation of the M value
>the green channel is used as reference by default.
>You can see it also by considering the corrispondent formula:
>(M = log(R/G) = log R - log G).
>
>In my  experiment, the red color is the reference
>so I was thinking that in this case I have to use some
>specific command to invert the M formula?
>
>Thank you!
>Giusy
>
>-----Original Message-----
>From: Naomi Altman [mailto:naomi at stat.psu.edu]
>Sent: Mon 2/9/2009 9:56 PM
>To: Giusy Della Gatta; bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] two color arrays normalization
>
>If there is no dye-swap, then what do you mean by "swapping of the colors"?
>
>--Naomi
>
>At 07:56 PM 2/9/2009, Giusy Della Gatta wrote:
>
> >Hi everybody,
> >
> >I am analyzing two color Agilent microarrays
> >by using LIMMA package.
> >In my specific case the red channel is representing
> >"the reference" while the green channel is "the treatment".
> >Is it enough to use the Target File composition to specify the name
> >of  the samples
> >and their corrispondet channels?  Or I have to use other specific commands
> >to specify the "swapping" of the colors?
> >
> >Thank you in advance!
> >Regards
> >Giusy
> >
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>
>Naomi S. Altman                                814-865-3791 (voice)
>Associate Professor
>Dept. of Statistics                              814-863-7114 (fax)
>Penn State University                         814-865-1348 (Statistics)
>University Park, PA 16802-2111

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111