Japan Bioinformatics

Simbiot use three sophisticated expression analysis function to analyze data from Affymetrix and Illumina cDNA microarrays.  Two functions are from Bioconductor (Gentleman, Carey et al. 2004): Limma (Smyth 2004) and LPE (Jain, Thatte et al. 2003), plus SAM (Tusher, Tibshirani et al. 2001) – one of the original expression analysis algorithms.  Simbiot’s implementation of SAM is based on the R version of the package .

 

References

Gentleman, R. C., V. J. Carey, et al. (2004). “Bioconductor: open software development for computational biology and bioinformatics.” Genome Biol 5(10): R80.

Jain, N., J. Thatte, et al. (2003). “Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays.” Bioinformatics 19(15): 1945-51.

Smyth, G. K. (2004). “Linear models and empirical bayes methods for assessing differential expression in microarray experiments.” Stat Appl Genet Mol Biol 3: Article3.

Tusher, V. G., R. Tibshirani, et al. (2001). “Significance analysis of microarrays applied to the ionizing radiation response.” Proc Natl Acad Sci U S A 98(9): 5116-21.

 

Selected screen shots