[BioC] RNA degradation plots

[James MacDonald]

One way is to simply color the lines using the col argument (e.g.,
plotAffyRNAdeg(AffyRNAdeg(abatch), col=1:14). You will only get 8 unique
colors, but they recycle so you should be able to figure out which one
is which. You could also add a legend (legend(x,y, lty=1, col=1:14,
legend=list.celfiles())).

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> <kfbargad at lg.ehu.es> 07/23/04 12:52PM >>>
Dear users,

I am working with 14 U133plus chips. I read in my data using ReadAffy()

and it was a bit slow but worked fine after having increased the memory

usage to 3000.

I have tried to obtain some degradation plots and this time the 
computer crashes. Is AffyRNADeg that demanding?

>Raw.Data <- ReadAffy()
>deg <- AffyRNADeg(Raw.Data)

I am running R 1.9.1 on a PC, 512megas RAM


Also, how could I label the outcome lines of plotAffyRNAdeg so that I 
graphically know which chip is the odd one in the case there is one? 
Maybe use the "legend" function, but how?

Thanks for your help

Regards

David

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