[BioC] Questions for Affy package on hist() and boxplot()

[James W. MacDonald]

Luo, Wen wrote:
> When using Affy package to QC the data with hist(), how to label the
> array id on the histogram to differentiate the multiple arrays on the
> same graph.

You can pass a vector of colors to hist(), as well as line types. For 
instance, if you have 16 arrays, you might do something like this:

hist(abatch, col=1:16, lty=c(rep(1,8), rep(2,8)) ## note that there will 
only be 8 colors plotted.
>  
> Our array id usually has a long name.  When using the boxplot(), how to
> rotate the label to be vertical, so the full array id could be seen.

See ?par and ?axis for more information.

boxplot(abatch, xaxt="n")
axis(1, las=2, label=sampleNames(abatch), cex.axis = 0.7)

Jim


>  
> This might be basic R questions, but I couldn't find the answer easily.
>  
> Thanks.
>  
> Wen
> 
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> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109