Hi, Just a quick question. I just noticed that boxplot(affybatch), returns values for n=5000. Is this correct? If so does this provide a sufficient description of all intensities on the chip, and how are the probesets(or probes?) selected. Also does hist(affybatch) also use less than all of the data? Is there a quick method to access summary stats, 5 number + mean, of the raw intensities? I'm using R 2.0 and BioC devel on ATH1 affy chips (22k probesets). Thanks, Matt

Yes boxplot(abatch) does only use 5000 of the intensity values. You can see how this is done by typing getMethods("boxplot") at an R prompt. I think a random sample of 5000 is sufficient to characterize perhaps 500,000 data points (if not, I guess we Statisticians should pack up our bag of tricks and go home!). This is sort of an ironic question, given the fact that most microarray experiments attempt to characterize the expression of thousands of genes for a potentially vast population, using maybe a total of 2 or 3 arrays. ;-D hist(abatch) does use all of the data points. Again, using getMethods("hist"), you can see that plotDensity.AffyBatch() is used to make the plot. Typing plotDensity.AffyBatch at an R prompt will show that there is no subsetting of the data. 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 >>> "Matthew Hannah" <hannah@mpimp-golm.mpg.de> 07/19/04 07:46AM >>> Hi, Just a quick question. I just noticed that boxplot(affybatch), returns values for n=5000. Is this correct? If so does this provide a sufficient description of all intensities on the chip, and how are the probesets(or probes?) selected. Also does hist(affybatch) also use less than all of the data? Is there a quick method to access summary stats, 5 number + mean, of the raw intensities? I'm using R 2.0 and BioC devel on ATH1 affy chips (22k probesets). Thanks, Matt _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor