[BioC] distribution of agilent array data.
chunxuan at outlook.com
Sun Nov 10 21:15:23 CET 2013
I am confused by the histogram of normalized Agilent microarray data.
It is human single color array, containing around 700 microarrays and 43K probes.
After normalization, I plotted the express value of all probes in single microarray, one example is attached.
I expected to see a more or less symmetric distribution, however, the values seems truncated. In the beginning I thought it may relate to offset value, but I have tried different value 16, 1, 0, still got similar distribution.
Any explanation or suggestions?
Here are codes for normalization:
targets <- readTargets("targets.txt")
x <- read.maimages(targets, source="agilent",green.only=TRUE)
y.bg <- backgroundCorrect(x, method="normexp")
y.bgn <- normalizeBetweenArrays(y.bg, method="quantile")
g.ex <- avereps(y.bgn, ID=y.bgn$genes$ProbeName)
da.norm <- g.ex$E
Here are R session:
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
attached base packages:
 graphics grDevices utils datasets stats methods base
other attached packages:
 ggplot2_0.9.3.1 reshape2_1.2.2 plyr_1.8
loaded via a namespace (and not attached):
 colorspace_1.2-4 dichromat_2.0-0 digest_0.6.3 grid_3.0.2 gtable_0.1.2 labeling_0.2
 MASS_7.3-29 munsell_0.4.2 proto_0.3-10 RColorBrewer_1.0-5 scales_0.2.3 stringr_0.6.2
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