R-Bioconductor is endowed with many features regarding microarrays quality analysis, however I would like to know if there is some material about the interpretation of the results bioC gives. For instance, how should I interpret the RNA DIGESTION PLOT? On my diagram I have a very high slope, I think; the first point, the average of the probecels equivalent between the probesets, has a value of 2, then it increases until the ninth that has a value of 12. Then the signal goes down until the last probe, the eleventh. The platform is a MOE430a. Is this diagram sufficient to say that I had a big Degradation? Is it worth to go on with the analysis? Isella Claudio

On Feb 5, 2005, at 7:16 AM, claudio..is@@libero..it wrote: > R-Bioconductor is endowed with many features regarding microarrays > quality > analysis, however I > would like to know if there is some material about the interpretation > of the > results bioC gives. > > For instance, how should I interpret the RNA DIGESTION PLOT? On my > diagram I > have a very high slope, I think; the first point, the average of the > probecels > equivalent between the probesets, has a value of 2, then it increases > until the > ninth that has a value of 12. Then the signal goes down until the last > probe, the > eleventh. The platform is a MOE430a. > Is this diagram sufficient to say that I had a big Degradation? Is it > worth to > go on with the analysis? > I believe that the slope, per se, is not that interesting. What you are looking for in this particular plot is whether the slope is really different for some samples versus others. If all are about the same, then things are probably ok. And if not, then you have a potential problem in that the arrays may not be directly comparable and some fancier work might be needed. Robert > Isella Claudio > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+