A Study on Two Group Comparison in Gene Expression Data

Tusher, Tibshirani and Chu (2001) suggested SAM (Significance Analysis of Microarrays) to compare two groups under different conditions for each gene, using microarray data. They used two sample t-statistic adding fudge factor in the denominator to prevent the value of statistic from being inflated by large sample variance, which might result in significant difference despite of a small value in the numerator. This paper aims at finding robust fudge factor and replacing it in two-sample t-statistic used in SAM, which we call Modified SAM (MSAM). Using the simulated data and data used in Dudoit et al.(2002), it is shown that MSAM find significant genes better and has less error rate than SAM.