Dear Bioconductor Users, I wish to view the histogram of RMA processed data to see if the RMA algorithm converged histograms of a number of slides and got rid of a bothersome second peak. When I apply the command > hist(howard1.norm) where howard1.norm is the output of the RMA command, > howard1.norm <-rma(howard1.raw) I get the following errormessage: Error in hist.default(howard1.norm) : `x' must be numeric Jim MacDonald pointed out to me that a file made with the command > dat1 <- normalize.AffyBatch.quantiles(dat) can have its histogram displayed. However I want to be able to see the histogram of dat processed by rma. Is there any command that I can use to display the histogram of data processed by the rma command? Thanks and best wishes, Rich ------------------------------------------------------------ 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'm giving up coffee. Now that it looks like I might top 6 feet, I don't want to risk spoiling it." - Isaac Friedman, age 14 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1732 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040513/034b0cfc/attachment.bin

Try plotDensity(exprs(howard1.norm)) 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 >>> Richard Friedman <friedman@cancercenter.columbia.edu> 05/13/04 10:02AM >>> Dear Bioconductor Users, I wish to view the histogram of RMA processed data to see if the RMA algorithm converged histograms of a number of slides and got rid of a bothersome second peak. When I apply the command > hist(howard1.norm) where howard1.norm is the output of the RMA command, > howard1.norm <-rma(howard1.raw) I get the following errormessage: Error in hist.default(howard1.norm) : `x' must be numeric Jim MacDonald pointed out to me that a file made with the command > dat1 <- normalize.AffyBatch.quantiles(dat) can have its histogram displayed. However I want to be able to see the histogram of dat processed by rma. Is there any command that I can use to display the histogram of data processed by the rma command? Thanks and best wishes, Rich ------------------------------------------------------------ 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'm giving up coffee. Now that it looks like I might top 6 feet, I don't want to risk spoiling it." - Isaac Friedman, age 14

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Ben, Here is the plot without the background correction: -------------- next part -------------- A non-text attachment was scrubbed... Name: howard1.norm4.nbg.pdf Type: application/pdf Size: 84406 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040513/f0f01034/howard1.norm4.nbg.pdf -------------- next part -------------- Do you advise me not to use the background correction in this case? Thanks and best wishes, Rich On May 13, 2004, at 11:32 AM, Ben Bolstad wrote: > One feature that is pretty striking is that you have a reasonable > amount > of saturation in your data (this is why you have the bump at the high > end). > > The weird biomodality (ignoring the small bump at the high end) is an > artifact of the background correction. Try this to see that disappear. > > howard1.norm <- rma(howard1.raw,background=FALSE) > plotDensity(exprs(howard1.norm)) > > > Ben > > > On Thu, 2004-05-13 at 08:20, Richard Friedman wrote: >> On May 13, 2004, at 10:35 AM, James MacDonald wrote: >> >> Try plotDensity(exprs(howard1.norm)) >> >> Jim >> >> >> >> Jim (and everybody), >> Jim, Thanks for your advice. >> I am somewhat puzzled at the outcome. Here is is the hist plot of >> theunnormalized data: >> >> hist(howard1.raw): >> >> >> ______________________________________________________________________ >> >> >> Here is the hist plot of the data normailzed by quanitles alone >> howard1.norm2<-normalize.AffyBatch.quantiles(howard1.raw) >> hist(howard1.norm2) >> >> >> ______________________________________________________________________ >> >> >> >> All of the plots were superimposed. However, i wanted to see >> thedistribution from >> RMA. So I followed your instructions. >> To the file howard1.norm that was created in the following way: >> >> howard1.norm <- rma(howard1.raw) >> I used the plotDensty command >> >> plotDensity(exprs(howard1.norm)) >> >> and got >> >> >> >> >> James W. MacDonald >> Affymetrix and cDNA Microarray Core >> >> >> ______________________________________________________________________ >> >> >> Shouldn't the distrubution be unimodal as in when just quantiles >> wasapplied? Also, is this this distrbution >> anything to worry about. >> >> Also, >> plotDensity(exprs(object))does not seem to be the equivalent of >> his(object). when I applied it to my raw dataset I got: >> >> >> ______________________________________________________________________ >> >> So, plotDensity doesn;t seem to be theequivalent of hist. >> Also, does the bimodal nature of the plotDensity of the rma plot >> pose a problem. It is trimodla if you count the blip at the end. >> >> Thanks and best wishes, >> Rich >> >> >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> >> Richard >> >> Friedman<friedman@cancercenter.columbia.edu> 05/13/04 >> 10:02AM >>> >> Dear Bioconductor Users, >> >> I wish to view the histogram of RMA processed data to >> see if the RMA algorithm converged histograms of a number of >> slides >> and got rid of a bothersome second peak. When I apply the >> command >> >> hist(howard1.norm) >> where howard1.norm is the output of the RMA command, >> >> howard1.norm <-rma(howard1.raw) >> >> I get the following errormessage: >> Error in hist.default(howard1.norm) : `x' must be numeric >> >> Jim MacDonald pointed out to me that a file made with the >> command >> >> dat1 <- normalize.AffyBatch.quantiles(dat) >> >> can have its histogram displayed. However I want to be able to >> see the >> histogram of dat processed by rma. >> >> Is there any command that I can use to display the histogram >> of data >> processed by the rma command? >> >> Thanks and best wishes, >> Rich >> ------------------------------------------------------------ >> 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'm giving up coffee. Now that it looks like I might top >> 6 feet, I don't want to risk spoiling it." >> - Isaac Friedman, age 14 >> >> ------------------------------------------------------------ >> 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'm giving up coffee. Now that it looks like I might top >> 6 feet, I don't want to risk spoiling it." >> - Isaac Friedman, age 14 >> >> >> >> ______________________________________________________________________ >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- > Ben Bolstad <bolstad@stat.berkeley.edu> > http://www.stat.berkeley.edu/~bolstad > > ------------------------------------------------------------ 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'm giving up coffee. Now that it looks like I might top 6 feet, I don't want to risk spoiling it." - Isaac Friedman, age 14