Hello all! I am having trouble interpreting whether my SAM outputs are valid enough that I should take them seriously, or whether to ignore them and try another method. Here is a sample of some of my output (samples are two-class paired samples; infected cells vs. non-infected cells with 3 different human donors for the cells; normalized with GCRMA): Gene set#1 D-value Q-value R-fold Gene 1 -179.854 0.410743 0.598795 Gene 2 -84.0229 0.417071 0.775385 Gene 3 -82.5916 0.417071 0.858212 Gene set#2 D-value Q-value R-fold Gene 4 86.7573 0.152039 1.00977 Gene 5 86.3523 0.152039 1.09908 Gene 6 -83.4252 0.152039 0.547529 How do I think about these results? I have several questions: (1) I am not too clear why the D-values are so high/low but the R-fold numbers are not bigger/smaller. I realize that the D-values are generated from the obs d(i) vs. the expect d(i) but I thought that this kind of related to the fold change? (2) For gene set #1, would the correct interpretation be that these genes are changing by "large" amounts but that since the q-values are so high (the FDR was around 0.4), they are not reliable? (3) Similarly for gene set #2, would the correct interpretation be that since the q-values are much lower (the FDR was about 0.2), one could be more confident that these are real changes that are being picked up? And if you were comfortable with a 20% chance that the genes you chose were falsely positive then you could move on to verify them? (4) What is being accepted for publication in terms of FDRs and q-values and such? It seems to me that that is really the defining answer. How low do the FDRs and q-values have to be before editors of journals will take the results seriously in people's experience?? Suggestions and/or advice here would be most welcome. Thank you!! ---Nick University of Iowa