[BioC] LIMMA - fold change direction?

Glyn Bradley glyn.bradley at googlemail.com
Thu Jul 17 17:42:17 CEST 2008

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)
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?


(ps I would've found it useful if 'coefficients' were labelled logFC
all the way through. But that might be due to my lack of stats

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