Hi all, this a pretty general question ... let say I have identified a set of genes differentially expressed between group A and group B and I m using Affy chips (but this could be also interesting for 2 color arrays). Is there a way - something already available) to see the distribution of these down and up-regulated genes (with 2 different colors) on the chip slides ? In addition, if we have "the impression" that the 2D distribution of these spots is not random with, for instance, a high density of these in the "left up corner" or somewhere else, is there a statistical test - so that it is no more an impression - to say that in some parts of the image, the distribution of these differentially expressed genes does not seem to be random suggesting a problem with the procedure or the slides ? I think that looking at the slides is necessary but not enought... ? Hoping that all this is understandable... Thanks Philippe [[alternative HTML version deleted]]

for cDNA this is easy. there are some functions in the packages for cDNA, e.g. in maImage in marrayPlots. but with affy the problem is that genes dont have locations. each of the 11-20 probes have a location. would you like to see the location of the probes for each gene? the function plotLocations can be used for this. On Wed, 21 Jan 2004 Phguardiol@aol.com wrote: > Hi all, > this a pretty general question ... > let say I have identified a set of genes differentially expressed between > group A and group B and I m using Affy chips (but this could be also interesting > for 2 color arrays). > Is there a way - something already available) to see the distribution of > these down and up-regulated genes (with 2 different colors) on the chip slides ? > In addition, if we have "the impression" that the 2D distribution of these > spots is not random with, for instance, a high density of these in the "left up > corner" or somewhere else, is there a statistical test - so that it is no more > an impression - to say that in some parts of the image, the distribution of > these differentially expressed genes does not seem to be random suggesting a > problem with the procedure or the slides ? I think that looking at the slides is > necessary but not enought... ? > Hoping that all this is understandable... > Thanks > Philippe > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

but with affy the problem is that genes dont have locations. each of the 11-20 probes have a location. would you like to see the location of the probes for each gene? the function plotLocations can be used for this. Yes, can we see the entire set of probes from all the genes/probesets differentially expressed, identified in a comparison test ? Is plot Locations going to tell us if there is a non random distribution of some of these ? This last question is also true for 2 color arrays. Is there any "spatial" tests already available for this kind of assessment ? Philippe [[alternative HTML version deleted]]

On Wed, Jan 21, 2004 at 01:53:43PM -0500, Phguardiol@aol.com wrote: > Hi all, > this a pretty general question ... > let say I have identified a set of genes differentially expressed between > group A and group B and I m using Affy chips (but this could be also interesting > for 2 color arrays). > Is there a way - something already available) to see the distribution of > these down and up-regulated genes (with 2 different colors) on the chip slides ? > In addition, if we have "the impression" that the 2D distribution of these > spots is not random with, for instance, a high density of these in the "left up > corner" or somewhere else, is there a statistical test - so that it is no more > an impression - to say that in some parts of the image, the distribution of > these differentially expressed genes does not seem to be random suggesting a > problem with the procedure or the slides ? Spatial statistics have certainly nifty things to use (point process analysis for example ?) > I think that looking at the slides is > necessary but not enought... ? Well, I would be believe that something obvious on a figure is meaningful... > Hoping that all this is understandable... >From your mail, I understand that you have the plots already (and do know about 'plotLocation', 'indices2xy' or friends). Explanations for the phenomenon can be multitple, and you are probably the best person to tell since you ran the experiments (or are in contact with the people who did). To give you ideas, here are examples of explanations: - chip not properly set during scanning (causing the confocal microscopes to be slightly out-of-focus a systematic way) - storage of the chips (say they are all piled with the same orientation, with one corner is close to heat/light/mobile phone... it has been seen with cDNA arrays) - the way the chips are handled during the process (finger pressing for example) Note that Affymetrix randomized the probe pairs across the chips because of such things (the Hu6800 for example was designed before that, and all the probes in a probe set are lined up) Hoping it helps, L. > Thanks > Philippe > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent