Normalization of oligonucleotide arrays based on the least-variant set of genes.

ABSTRACT:

Background

It is well known that the normalization step of microarray data makes a difference in the downstream analysis. All normalization methods rely on certain assumptions, so differences in results can be traced to different sensitivities to violation of the assumptions. Illustrating the lack of robustness, in a striking spike-in experiment all existing normalization methods fail because of an imbalance between up- and down-regulated genes. This means it is still important to develop a normalization method that is robust against violation of the standard assumptions

Results

We develop a new algorithm based on identification of the least-variant set (LVS) of genes across the arrays. The array-to-array variation is evaluated in the robust linear model fit of pre-normalize

SUBMITTER: Calza S 

PROVIDER: S-EPMC2324100 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature