[BioC] Limma - using both array and spot weights in lmFit

[Jakob Hedegaard]

Hi List

I use spot weights (binary) to A) ignore spots "Not found" in GenePix during normalization:

RG <- read.maimages(fnames, source="genepix", path=datadir, columns=columns, other.columns=other.columns, wt.fun=wtflags(weight=0,cutoff=0))
MA <- normalizeWithinArrays(RG, method="loess", weights=RG$weights, bc.method="none")

... and B) include "cDNA" spots only in lmFit (ignoring various control spots):

MA$weights[MA$genes$Status!="cDNA",] <- 0
fit <- lmFit(MA, design, ndups=2, weights=MA$weights, method="robust", correlation=cor$cor)


Does the use of array weights in lmFit...

arrayw <- arrayWeights(MA, design, weights=MA$weights)
fit2 <- lmFit(MA, design, ndups=2, weights=arrayw, method="robust", correlation=cor$cor)

... exclude the individual spot weights? 

Are all spots from an "array weighted" array given the same weight in lmFit - thereby ignoring the "original" spot weights (in MA$weights)?

How can the various control spots then be ignored in lmFit?



> arrayw
        1         2         3         4         5         6         7         8
0.9003237 0.5224861 0.8302243 0.7377452 0.6727376 1.1749278 1.0347314 0.4233758
        9        10        11        12        13        14        15        16
0.5922037 0.5770843 1.1066639 0.5070331 1.1136625 0.8131061 0.9608490 0.3578452
............
       81        82        83        84        85        86        87        88
1.1762249 0.8947206 1.0537712 1.2835124 1.4650973 1.8305352 1.4610934 1.4539068
       89        90        91        92        93        94        95        96
1.3118581 1.1803798 1.5399506 1.2547482 1.3258992 1.0470026 1.0130834 1.1672451


> sessionInfo()
R version 2.4.1 (2006-12-18)
x86_64-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"

other attached packages:
    MASS  statmod      GDD    limma
"7.2-30"  "1.3.0"  "0.1-8" "2.9.16"



Looking forward hearing from you

Jakob Hedegaard
Project scientist
 	
UNIVERSITY OF AARHUS	
Faculty of Agricultural Sciences	
Dept. of Genetics and Biotechnology	
Blichers Allé 20, P.O. BOX 50	
DK-8830 Tjele