[BioC] unnormalised vs normalised distribution

[Jenny Drnevich]

There was just a lengthy exchange on this subject earlier this week - check 
the Bioconductor Archives https://stat.ethz.ch/pipermail/bioconductor/ for 
"RMA biomodality"

Jenny

At 08:13 AM 6/9/2006, Michal Okoniewski wrote:
>Benjamin,
>
>And what do you get when you use standard RMA instead of GCRMA?
>I have run GCRMA on my data and see similar pattern - the second peak
>is small, but is there. In general GCRMA seems to result in much more
>small values - RMA has a bit "nicer" distribution.
>
>Once I've run a distribution of correlation of all probesets against
>all.
>For MAS and RMA I got what I expected - almost normal distribution,
>slightly shifted towards positive r. For GCRMA the distribution
>had not really normal shape (almost symmetric convex function with the
>maximum roughly in the same place as RMA - close to 0). From that time
>on, I believe that GCRMA may impose some artifacts onto data...
>
>Cheers,
>Michal
>
>-----Original Message-----
>From: bioconductor-bounces at stat.math.ethz.ch
>[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of botto
>Sent: 08 June 2006 13:24
>To: bioconductor at stat.math.ethz.ch
>Subject: [BioC] unnormalised vs normalised distribution
>
>Dear list members,
>
>I've been looking at the distribution plots of pm intensities and the
>corresponding expression values calculated by gcrma for a certain data
>set. Now I'm wondering what the best interpretation of these plots would
>be, because the former looks quite usual while the latter seems quite
>"unfamiliar" to me (nearly like a bimodal distribution, a jpg file
>should be attached). The data measured is simply the expression for
>certain mouse tumor tissues. Can anybody explain why after the
>background correction and normalisation I get this distribution shape?
>
>log(PM) density:
>
>|      *
>|    *  *
>|   *    *
>|  *     *
>|  *      *
>| *        *
>|*          *
>|             ***********
>+-------------------------------
>
>gcrma-expression values:
>
>|      *
>|    *  *
>|   *    *
>|  *     *
>|  *      *
>| *        *     * * *
>|*          ****       *
>|                        ***
>+----------------------------------
>
>
>
>
>
>--
>Benjamin Otto
>Universitaetsklinikum Eppendorf Hamburg
>Institut fuer Klinische Chemie
>Martinistrasse 52
>20246 Hamburg
>
>--------------------------------------------------------
>
>
>This email is confidential and intended solely for the use o...{{dropped}}
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
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e-mail: drnevich at uiuc.edu