High throughput technologies, such as gene expression arrays and protein mass spectrometry, allow one to simultaneously evaluate thousands of potential biomarkers that could distinguish different tissue types. Of particular interest here is distinguishing between cancerous and normal organ tissues. We consider statistical methods to rank genes (or proteins) in regards to differential expression...

MOTIVATION It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation. RESULTS We developed two methods which are mainly based on the q-values approach; the first is a direct extension of the q-values approach, while the second uses two approaches: q-values and maximum-likelihood. We present two algorithms for the second me...

In this vignette, we show how the functions contained in the R package siggenes can be used to perform both the Significance Analysis of Microarrays (SAM) proposed by Tusher et al. (2001) and the Empirical Bayes Analysis of Microarrays (EBAM) suggested by Efron et al. (2001).