retation of p-values can differ depending on the desired analytic stringency, one may choose to modify an alpha or a gamma cutoff. For example, if you would like to make Present calls associated with more stringent Detection p-values, you can set alpha1 to a lower level, say 0.025. Doing so will decrease the number of Present calls by converting those with p-values in the range 0.025-0.04 to Marginal calls. There will be a sensitivity vs. specificity tradeoff, since some of the calls that became Marginal may be falsely detected genes, but some may also be truly expressed genes. If you do modify the alpha or gamma cutoffs, it is advisable to maintain the p-values with the calls since they are not affected by an alpha or gamma parameter change.
1) Liu, W., Mei, R., Di, X., Ryder, TB., Hubbell, E., Dee, S., Webster, T., Ho, M., Baid, J., and Smeekens, SP. Analysis of high density expression microarrays with signed-rank call algorithms, manuscript, 2001.
2) Affymetrix Technical Note 1, New Statistical Algorithms for Monitoring Gene Expression on GeneChip Probe Arrays. Part Number 701097.
3) Jin, H., Yang, R., Awad, TA., Wang, F., Li, W., Williams, SP., Ogasawara, A., Shimada, B., Williams PM., Gianfranco de Feo, G., Paoni, NF. Effects of Early Angiotensin-Converting Enzyme Inhibition on Cardiac Gene Expression After Acute Myocardial Infarction. Circulation, 103:736, 2001
4) Statistical Algorithms Reference Guide. Part Number 701110.
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