[BioC] limma design and biolrep matrix, duplicateCorrelation
Glyn Bradley
gbradley at mycib.ac.uk
Thu Aug 14 17:48:23 CEST 2008
Hi all
Sorry I've asked on this topic before but I'm still confused.
This time...
6 Imagene arrays. Targets file :
"Name " "FileNameCy3" "FileNameCy5"
"Cy3" "Cy5"
"5636-T56-Br.1-3.txt"
"5636-P119-Br.1-5.txt" "T56" "P119"
"2280-P119-Br.1-3.txt" "2280-T56-Br.1-5.txt"
"p119" "T56"
"9187-T56-Br.2-3.txt"
"9187-P119-Br.2-5.txT" "T56" "P119"
"7157-P119-Br.2-3.txt"
"7157-T56-Br.2-5.txt" "p119" "T56"
"9189-T56-Br.4-3.txt"
"9189-P119-Br.2-5.txt" "T56" "P119"
2282-P119-Br.1-3.txt"
"2282-T56-Br.3-5.txt" "p119" "T56"
1&2 and 3&4 are technical replicates (dye-swaps), 5&6, though dye swaps,
are also different biological samples .
so is this correct?
design <- c(1, -1, 1, -1, 1, -1)
biolrep <- c(1, 1, 2, 2, 3, 4)
and can I use duplicatedCorrelation?...
corfit <- duplicateCorrelation(MA, design, ndups = 1, block = biolrep)
fit <- lmFit(MA, design, block = biolrep, cor = corfit$consensus)
(I get over 50 warnings when I do use duplicateCorrelation)
Thanks
Glyn
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