Ben,
Here is the plot without the background correction:
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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