Hi All, I am attaching a PDF of boxplot for my data,x-axis is the file names but what is the y-axis?! Also only some of the file names show up? Thanks, Hrishi __________________________________________________ -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_normal.pdf Type: application/pdf Size: 28149 bytes Desc: boxplot_normal.pdf Url : https://stat.ethz.ch/pipermail/bioconductor/attachments/20050318 /0fcb38c0/boxplot_normal.pdf

Dear Hirshi, The Y axis gives the quantile distribution of each slide. The vertical line is the median. The colored boxes are the number of intensities that fall within a certain range (I don't know what % here). For normalized data both the means and the boxes should pretty much line up. On the X axis they refer to X01.Cel X02.CEL etc. I hope that this helps, Rich On Mar 18, 2005, at 1:41 PM, Hrishikesh Deshmukh wrote: > Hi All, > > I am attaching a PDF of boxplot for my data,x-axis is > the file names but what is the y-axis?! Also only some > of the file names show up? > > Thanks, > Hrishi > > __________________________________________________ > > > <boxplot_normal.pdf>_______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "I would do more in the house, but you always beat me to it". -Isaac Friedman, age 15

That depends on what you did a boxplot on. It could be the values in the CEL files if you did the boxplot on AffyBatch or it could be the values of the expression measure if you did it on an exprSet. For more info on what a boxplot shows see help("boxplot"). One way you can get around the problem with x-axis labels is to suppress it and then place mtext() as such. plot( 1:10, xaxt="n" ) # suppress the x-axis par(las=2) # rotate labels 90 degree mylabels <- paste("Sample", 1:10) mtext( mylabels, side=1, line=0.5, at=1:10, srt=270 ) Regards, Adai On Fri, 2005-03-18 at 10:41 -0800, Hrishikesh Deshmukh wrote: > Hi All, > > I am attaching a PDF of boxplot for my data,x-axis is > the file names but what is the y-axis?! Also only some > of the file names show up? > > Thanks, > Hrishi > > __________________________________________________ > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor