Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays.

ABSTRACT:

Background

Alternative splicing is an important mechanism that increases protein diversity and functionality in higher eukaryotes. Affymetrix exon arrays are a commercialized platform used to detect alternative splicing on a genome-wide scale. Two probe summarization algorithms, PLIER (Probe Logarithmic Intensity Error) and RMA (Robust Multichip Average), are commonly used to compute gene-level and exon-level expression values. However, a systematic comparison of these two algorithms on their effects on high-level analysis of the arrays has not yet been reported.

Results

In this study, we showed that PLIER summarization led to over-estimation of gene-level expression changes, relative to exon-level expression changes, in two-group comparisons. Consequently, it led to detecti

SUBMITTER: Qu Y 

PROVIDER: S-EPMC2873539 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature