The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies.

ABSTRACT:

Background

Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers.

Results

Using two publicly available datasets, i.e., gene-expression data of 285 patients with Acute Myeloid Leukemia (AML, Affym

SUBMITTER: Verhaak RG 

PROVIDER: S-EPMC1481623 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature