IMAGE PLOTS.
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@stephen-nyangoma-366
Last seen 10.3 years ago
Hi all, I am doing image plots of affy chips but cannot get a good refference for interpretations. I have read the manual but all it says is that you can examine the quality of the intensities from it. It does not explain what is plotted, for example. Does the image plot depict both PM and MMMs or just PMs. Are the intensities log transformed? How is it constructed? Is it realted to the hist plot (which is just a histogram of the logged PM intensities on a chip)? Thanks for your help. Stephen.
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Laurent Gautier ★ 2.3k
@laurent-gautier-29
Last seen 10.3 years ago
On Wed, Jan 21, 2004 at 09:04:16PM +0100, Stephen Nyangoma wrote: > Hi all, > I am doing image plots of affy chips but cannot get a good refference > for interpretations. I have read the manual but all it says is that you > can examine the quality of the intensities from it. It does not explain > what is plotted, for example. Does the image plot depict both PM and > MMMs or just PMs. Are the intensities log transformed? How is it > constructed? Is it realted to the hist plot (which is just a histogram > of the logged PM intensities on a chip)? > > Thanks for your help. > > > Stephen. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor The images are simply probe intensities at their respective X/Y coordinates. The intensity are encoded by colors. *all the probe intensities* in CEL files are plotted (PM/MM/unknown). One can specify a transformation to apply on probe intensities prior to color encoding. If I remember right, the default transformation was set to 'log' not so long ago. The default coloring is a grey scale. Examples of such image plots showing experimental artefacts can be found in Chapter 4 of 'Analysis of Gene Expression Data, Methods and Software' (Springer), or in the forthcoming article 'affy - Analysis of Affymetrix GeneChip data at the probe level' (Bioinformatics, Feb. 2004). Hoping it helps, Laurent -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
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Thanks, Laurent. I got the solution by applying plotLocation() command. Using this one can see that the image plot includes both MMs and PMs. Stephen. Quoting Laurent Gautier <laurent@cbs.dtu.dk>: > On Wed, Jan 21, 2004 at 09:04:16PM +0100, Stephen Nyangoma wrote: > > Hi all, > > I am doing image plots of affy chips but cannot get a good refference > > for interpretations. I have read the manual but all it says is that you > > can examine the quality of the intensities from it. It does not explain > > what is plotted, for example. Does the image plot depict both PM and > > MMMs or just PMs. Are the intensities log transformed? How is it > > constructed? Is it realted to the hist plot (which is just a histogram > > of the logged PM intensities on a chip)? > > > > Thanks for your help. > > > > > > Stephen. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > The images are simply probe intensities at their respective X/Y > coordinates. > The intensity are encoded by colors. *all the probe intensities* in CEL > files are plotted (PM/MM/unknown). One can specify a transformation to > apply on probe intensities prior to color encoding. If I remember right, > the default transformation was set to 'log' not so long ago. The default > coloring is a grey scale. > > Examples of such image plots showing experimental artefacts can be found > in Chapter 4 of 'Analysis of Gene Expression Data, Methods and Software' > (Springer), or in the forthcoming article 'affy - Analysis of Affymetrix > GeneChip data at the probe level' (Bioinformatics, Feb. 2004). > > > Hoping it helps, > > > > Laurent > > > > -- > -------------------------------------------------------------- > Laurent Gautier CBS, Building 208, DTU > PhD. Student DK-2800 Lyngby,Denmark > tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
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