Display of histogram of RMA-processed data
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@richard-friedman-513
Last seen 7.7 years ago
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
Cancer Cancer • 955 views
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@james-w-macdonald-5106
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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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@richard-friedman-513
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Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: howard1.raw.hist.pdf Type: application/pdf Size: 82927 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040513/0713c419/howard1.raw.hist.pdf -------------- next part -------------- Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: howard.norm2.hist.pdf Type: application/pdf Size: 62205 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040513/0713c419/howard.norm2.hist.pdf -------------- next part -------------- Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: howard1.norm.plotdensity.pdf Type: application/pdf Size: 86355 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040513/0713c419/howard1.norm.plotdensity.pdf -------------- next part -------------- Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: howard1,raw.plotDensity.pdf Type: application/pdf Size: 73852 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040513/0713c419/howard1raw.plotDensity.pdf -------------- next part -------------- Skipped content of type multipart/alternative
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Hello all I have seen such post RMA hist plots in my data too (human tumours on U133A chips). I did not see a nice smooth curve but curves that looked very similar to yours (two peaks etc). I think there is nothing wrong with the data, it probably has to do with the way you plot it. Indeed, if you use plot(density(exprs(rma), bw="nrd0", adjust=1)) instead and play around with the adjust value you will see that you can actually smoothen the way the data looks in the plots. This actually alters the width used for plotting I believe (?). I would be interested to hear what everybody thinks about this. Yours kindly, Lawrence _______________________________ Lawrence-Paul Petalidis Ph.D Candidate Department of Pathology Division of Molecular Histopathology University of Cambridge _______________________________ -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Richard Friedman Sent: 13 May 2004 16:21 To: James MacDonald Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Display of histogram of RMA-processed data 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 the unnormalized data: hist(howard1.raw): << File: howard1.raw.hist.pdf >> << File: howard.norm2.hist.pdf >> << File: howard1.norm.plotdensity.pdf >> << File: howard1,raw.plotDensity.pdf >> [[alternative HTML version deleted]]
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if the concern is the last little bump for high concentrations, that is most likely due to saturation. this is usually due to some scanner tunning parameter being too high. no preprocession algorithm will (or should) get rid of that. On Thu, 13 May 2004, 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 the > unnormalized data: > > hist(howard1.raw): >
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@richard-friedman-513
Last seen 7.7 years ago