[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-P119-Br.1-5.txt"    "T56"    "P119"
                    "2280-P119-Br.1-3.txt"      "2280-T56-Br.1-5.txt"    
"p119"    "T56"
"9187-P119-Br.2-5.txT"    "T56"    "P119"
"7157-T56-Br.2-5.txt"    "p119"    "T56"
"9189-P119-Br.2-5.txt"    "T56"    "P119"
"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)



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