[BioC] RNA degradation plots

James MacDonald jmacdon at med.umich.edu
Fri Jul 23 19:48:14 CEST 2004

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,



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

>>> <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



Bioconductor mailing list
Bioconductor at stat.math.ethz.ch 

More information about the Bioconductor mailing list