Salvaging Affymetrix probes after probe-level re-annotation.

ABSTRACT:

Background

Affymetrix GeneChips can be re-annotated at the probe-level by breaking up the original probe-sets and recomposing new probe-sets based on up-to-date genomic knowledge, such as available in Entrez Gene. This results in custom Chip Description Files (CDF). Using these custom CDFs improves the quality of the data and thus the results of related gene expression studies. However, 44-71% of the probes on a GeneChip are lost in this re-annotation process. Although generally aimed at less known genes, losing these probes obviously means a substantial loss of expensive experiment data. Biologists are therefore very reluctant to adopt this approach.

Findings

We aimed to re-introduce the non-affected Affymetrix probe-sets after these re-annotation procedures. For this, we d

SUBMITTER: de Leeuw WC 

PROVIDER: S-EPMC2547102 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature