[BioC] LIMMA - fold change direction?

[J.delasHeras at ed.ac.uk]

Quoting Glyn Bradley <glyn.bradley at googlemail.com>:

> Hi all
>
> 3 bio replicate and dye swap cDNA array experiment comparing 17day and
> 27day samples being analyzed with limma
> targets file:
> "Name"	"FileNameCy3"	"FileNameCy5"	"Cy3"	"Cy5"
> 	"1-Cy3-Ac-17d.txt"	"1-Cy5-Ac-27d.txt"	"17day"	"27day"
> 	"2-Cy3-Ac-27d.txt"	"2-Cy5-Ac-17d.txt"	"27day"	"17day"
> 	"3-Cy3-Ac-17d.txt"	"3-Cy5-Ac-27d.txt"	"17day"	"27day"
> 	"4-Cy3-Ac27d.txt"	"4-Cy5-Ac17d.txt"	"27day"	"17day"
> 	"5-Cy3-Ac17d.txt"	"5-Cy5-Ac27d.txt"	"17day"	"27day"
> 	"6-Cy3-Ac27d.txt"	"6-Cy5-Ac17d.txt"	"27day"	"17day"
>
> so after
> ...
> RG <- read.maimages(files, source="imagene")
> MA <- normalizeWithinArrays(RG)
> design=c(1,-1,1,-1,1,-1)
> fit <- lmFit(MA, design)
> .
> what direct are the fold changes I get out in
> does a positive FC mean up regulated in the 27day sample?
>
> Thanks

If in doubt, and you don't understand the design matrix, you can  
simply find a probe with a large positive M value, and then look at  
the raw intensities for that one. Then it will be obvious.

Jose


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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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