[BioC] Agilent 2 colour spike-in controls

Nathan S. Watson-Haigh nathan.watson-haigh at csiro.au
Thu May 7 12:25:47 CEST 2009

A quick question and hopefully a quick answer in reply....

I have data from Agilent bovine chips. Are the spike-in probe replicates
(of which there are 32 on each chip) supposed to be highly replicable on
an MA plot? Some of my chips show good reproducibility of the spike-in's
on MA plots, but others show streaks running bottom left to top right on
the MA plot. I'm wondering if this may indicate problems with some of
the chips!?

Find my code below.


My SpotTypes.txt file is like:

SpotType        ControlType     ProbeName       col
Other   *       *       white
Probe   0       *       black
Negative        -1      *3xSLv1*        blue
E1A 1   1       *E1A_r60_1$     red
E1A n11 1       *E1A_r60_n11$   pink
E1A a20 1       *E1A_r60_a20$   brown
E1A 3   1       *E1A_r60_3$     orange
E1A a104        1       *E1A_r60_a104$  yellow
E1A a107        1       *E1A_r60_a107$  green
E1A a135        1       *E1A_r60_a135$  blueviolet
E1A a22 1       *E1A_r60_a22$   cyan
E1A a97 1       *E1A_r60_a97$   bisque4
E1A n9  1       *E1A_r60_n9$    aquamarine

RG <- read.maimages(files=targets$FileName, source="agilent",
names=targets$Name, )
spottypes <- readSpotTypes()
RG$genes$Status <- controlStatus(spottypes, RG)

nArrays <- ncol(RG)
png(file = "Raw_MA.png", type = "cairo1",
width=5*ceiling(sqrt(nArrays)), height=5*ceiling(sqrt(nArrays)),
units="in", res=300)
par(mfrow=c(ceiling(sqrt(nArrays)), ceiling(sqrt(nArrays))),
for(i in 1:nArrays) {
        plotMA(RG, array=i, pch=16)

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