[BioC] How does limma know how to correct dye effect with a column of "1"s

[Claus-Dieter Mayer]

Hi Nigel,

Limma models the log-ratio (log(Cy5/Cy3)) between the two channels; the 
columns of 1's mean that you include a constant (an intercept) in your 
model that has to be added to the mean whatever level of your other 
factors (time, treatment, you name it...) you have, i.e even if you had 
the same conditions on Cy5 and Cy3 that effect would still be there. 
Which means it is the dye-effect!

Claus

Ng Stanley wrote:
> Hi,
>
> In chapter 8.1.2 Dye swaps, why does appending a column of "1"s as part of
> the design matrix take into account the dye effect ? How does limma know
> this column of "1"s is for the dye-effect and not some other variablity ? I
> can argue that "1"s could represent time effect, and time effect occur.
>
> Thanks
> Stanley
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>
>
>
> Click link below to report this email as spam.
> https://www.mailcontrol.com/sr/LfbPOsYxEWQfdeM5Ynvp06uPr0Mrv8Q0+aWee1Wmo7!kEDU3tN8wf3HJwbvHyVjNDwp+DyY8zsTSyBdGqJafbiYwhYRZcfmElfwwY7+nRPHyWE672gsfPzPDVR4Gpf9bDOcGee3ZHcjZ6tMTMBamPs5OcJsL!hF8AO0dRVnq1sIy+ykk0Pzmd7wkPAexOkg8WleOeRFGiOlWQcLMIAU6IvDa8+GUGke!  
>
>
>   

-- 
***********************************************************************************
 Dr Claus-D. Mayer                    | http://www.bioss.ac.uk
 Biomathematics & Statistics Scotland | email: claus at bioss.ac.uk
 Rowett Research Institute            | Telephone: +44 (0) 1224 716652
 Aberdeen AB21 9SB, Scotland, UK.     | Fax: +44 (0) 1224 715349