We seem to get quite a few questions of the following type: >Are they the genes up/down regulated due to sample A or sample B? As a statistician, I want to urge you to LOOK at your data before (or at least along with) your p-values. For at least a few of your significant and nonsignificant genes, you should look at the normalized data and the treatment means and make sure that the results are sensible. I have been a statistician for over 25 years, and I still do this with EVERY analysis I do. Firstly, it helps you decide if there is something wrong with the data - e.g. big outliers that are affecting the analysis, or missing values that really should be there, or the wrong column of the data selected. Secondly, it helps you understand features of the analysis, such as whether the genes have been up or down regulated, or why certain interactions are important. Finally, (and perhaps I am less careful than others), errors often creep into my analysis steps and these are usually obvious if I look at the data along with the results, rather than just the results. (For example, I once failed to notice that an investigator had used 9999 as a missing value code - we had some highly significant results due to including this as valid data.) >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

Hello everybody. I use Bioconductor daily to analyze data provided by the lab. Im going to a national conferance in bioinformatics and want to advertise for Bioconductor. This may be an odd question but: am I allowed to make a poster describing Bioconducor and some of its packages on some data? (I will of cource cite the appropriate papers and authours of packages) morten