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. 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. This might be basic R questions, but I couldn't find the answer easily. Thanks. Wen [[alternative HTML version deleted]]

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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109

Hi James, Thanks for your help. Your solution for the boxplot() works well. For the hist(), what I would like to do is labeling the histogram of each array with the corresponding array name. Thanks. Wen -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Thursday, February 03, 2005 1:34 PM To: Luo, Wen Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Questions for Affy package on hist() and boxplot() 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109