Identification of Significant Differential Expression
Many strategies exist to identify which array probes show an unusual level of over expression or under expression. The simplest one is to call "significant" any probe that differs by an average of at least twofold between treatment groups. More sophisticated approaches are often related to t-tests or other mechanisms that take both effect size and variability into account. Curiously, the p-values associated with particular genes do not reproduce well between replicate experiments, and lists generated by straight fold change perform much better. This represents an extremely important observation, since the point of performing experiments has to do with predicting general behavior. The MAQC group recommends using a fold change assessment plus a non-stringent p-value cutoff, further pointing out that changes in the background correction and scaling process have only a minimal impact on the rank order of fold change differences, but a substantial impact on p-values.
Read more about this topic: Microarray Analysis Techniques
Famous quotes containing the words significant, differential and/or expression:
“Play permits the child to resolve in symbolic form unsolved problems of the past and to cope directly or symbolically with present concerns. It is also his most significant tool for preparing himself for the future and its tasks.”
—Bruno Bettelheim (20th century)
“But how is one to make a scientist understand that there is something unalterably deranged about differential calculus, quantum theory, or the obscene and so inanely liturgical ordeals of the precession of the equinoxes.”
—Antonin Artaud (1896–1948)
“But the wise know that foolish legislation is a rope of sand, which perishes in the twisting; that the State must follow, and not lead the character and progress of the citizen; the strongest usurper is quickly got rid of; and they only who build on Ideas, build for eternity; and that the form of government which prevails, is the expression of what cultivation exists in the population which permits it.”
—Ralph Waldo Emerson (1803–1882)