[BioC] distribution of agilent array data.‏

shao chunxuan hibergo at outlook.com
Sun Nov 10 21:19:44 CET 2013

Hi everyone, 

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. 

 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)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] ggplot2_0.9.3.1 reshape2_1.2.2  plyr_1.8       

loaded via a namespace (and not attached):
 [1] colorspace_1.2-4   dichromat_2.0-0    digest_0.6.3       grid_3.0.2         gtable_0.1.2       labeling_0.2      
 [7] 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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