Dear gurus: Sorry for this off-topic question. I am thinking if it is a good idea to remove low-intensity probesets of affymetrix. For example, the following is a part of summary of log2 intensity from the u133a probesets across 81 samples: 1007_s_at 1053_at 117_at 121_at Min. : 5.966 Min. :4.635 Min. :2.925 Min. :2.466 1st Qu.: 8.194 1st Qu.:5.366 1st Qu.:3.381 1st Qu.:2.553 Median : 8.873 Median :5.570 Median :3.509 Median :2.604 Mean : 8.824 Mean :5.639 Mean :3.816 Mean :2.801 3rd Qu.: 9.522 3rd Qu.:5.898 3rd Qu.:3.919 3rd Qu.:2.860 Max. :11.132 Max. :7.094 Max. :6.650 Max. :3.828 My question is, does it make sense to remove the probeset 121_at for its max(log2 intensity) is only 3.828? thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III