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PMID: 12582260 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Summaries of Affymetrix GeneChip probe level data.

Nucleic acids research ·Vol. 31 ·No. 4 ·2003-02-15 ·Pages e15

Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP

Abstract

High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to obtain expression measures it is necessary to summarize the probe level data. Using two extensive spike-in studies and a dilution study, we developed a set of tools for assessing the effectiveness of expression measures. We found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models. In particular, improvements in the ability to detect differentially expressed genes are demonstrated.

MeSH Terms

Central Nervous System/metabolism DNA Probes/genetics,standards Gene Expression Profiling Humans Liver/metabolism Oligonucleotide Array Sequence Analysis/methods,standards RNA, Messenger/genetics,metabolism Reproducibility of Results Software

Chemicals

DNA Probes RNA, Messenger

Authors & Affiliations

6 authors, click to expand affiliations / ORCID

Irizarry Rafael A

Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA. rafa@jhu.edu

Bolstad Benjamin M

Collin Francois

Cope Leslie M

Hobbs Bridget

Speed Terence P

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13 references, click to expand

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Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gng015

rafa@jhu.edu

Published

2003-02-15

Pages

e15

Language

English

Region

England

NLM ID

0411011

PMCID

PMC150247

Subset

Grants

NHLBI NIH HHS · U01 HL066583 · United States

NHLBI NIH HHS · U01 HL66583 · United States

External Links

PubMed source DOI: 10.1093/nar/gng015 PMC Full Text View journal details

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