Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements.

ABSTRACT:

Background

Affymetrix GeneChip microarrays are popular platforms for expression profiling in two types of studies: detection of differential expression computed by p-values of t-test and estimation of fold change between analyzed groups. There are many different preprocessing algorithms for summarizing Affymetrix data. The main goal of these methods is to remove effects of non-specific hybridization, and to optimally combine information from multiple probes annotated to the same transcript. The methods are benchmarked by comparison with reference methods, such as quantitative reverse-transcription PCR (qRT-PCR).

Results

We present a comprehensive analysis of agreement between Affymetrix GeneChip and qRT-PCR results. We analyzed the influence of filtering by fraction Present

SUBMITTER: Mieczkowski J 

PROVIDER: S-EPMC2841208 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature