Variance-stabilizing transformations for two-color microarrays

B. P. Durbin, D. M. Rocke
2004 Bioinformatics  
Motivation: Authors of several recent papers have independently introduced a family of transformations (the generalizedlog family), which stabilizes the variance of microarray data up to the first order. However, for data from two-color arrays, tests for differential expression may require that the variance of the difference of transformed observations be constant, rather than that of the transformed observations themselves. Results: We introduce a transformation within the generalizedlog
more » ... eneralizedlog family which stabilizes, to the first order, the variance of the difference of transformed observations. We also introduce transformations from the 'started-log' and log-linear-hybrid families which provide good approximate variance stabilization of differences. Examples using control-control data show that any of these transformations may provide sufficient variance stabilization for practical applications, and all perform well compared to log ratios.
doi:10.1093/bioinformatics/btg464 pmid:15033873 fatcat:rbbz3meu2zci5nm2gf57mkapgq