Pre-processing Agilent microarray data.

Pre-processing Agilent microarray data. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Pre-processing Agilent microarray data. Abstract Text:

Marianna Zahurak,Giovanni Parmigiani,Wayne Yu,Robert B Scharpf,David Berman,Edward Schaeffer,Shabana Shabbeer,Leslie Cope,

BACKGROUND: Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error that affect measurement of expression using Agilent arrays and to compare Agilent's Feature Extraction software with pre-processing methods that have become the standard for normalization of cDNA arrays. These include log transformation followed by loess normalization with or without background subtraction and often a between array scale normalization procedure. The larger goal is to define best study design and pre-processing practices for Agilent arrays, and we offer some suggestions. RESULTS: Simple loess normalization without background subtraction produced the lowest variability. However, without background subtraction, fold changes were biased towards zero, particularly at low intensities. ROC analysis of a spike-in experiment showed that differentially expressed genes are most reliably detected when background is not subtracted. Loess normalization and no background subtraction yielded an AUC of 99.7% compared with 88.8% for Agilent processed fold changes. All methods performed well when error was taken into account by t- or z-statistics, AUCs > or = 99.8%. A substantial proportion of genes showed dye effects, 43% (99% CI: 39%, 47%). However, these effects were generally small regardless of the pre-processing method. CONCLUSION: Simple loess normalization without background subtraction resulted in low variance fold changes that more reliably ranked gene expression than the other methods. While t-statistics and other measures that take variation into account, including Agilent's z-statistic, can also be used to reliably select differentially expressed genes, fold changes are a standard measure of differential expression for exploratory work, cross platform comparison, and biological interpretation and can not be entirely replaced. Although dye effects are small for most genes, many array features are affected. Therefore, an experimental design that incorporates dye swaps or a common reference could be valuable.

Pre-processing Agilent microarray data. Publishing Authors By Initials

M Zahurak,G Parmigiani,W Yu,RB Scharpf,D Berman,E Schaeffer,S Shabbeer,L Cope,

For similar investigative techniques: chemistry, analytical: microchip analytical procedures: microarray analysis: oligonucleotide array sequence analysis research abstracts see: investigative techniques: chemistry, analytical: microchip analytical procedures: microarray analysis: oligonucleotide array sequence analysis research

PUBMED ID PMID:

MEDLINE DATE:

Pre-processing Agilent microarray data. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: BMC bioinformatics

VOLUME: 8

Page Numbers: 142

Journal Abbreviation: BMC Bioinformatics

ISSN: 1471-2105

DAY: 1

MONTH: 05

YEAR: 2007

Pre-processing Agilent microarray data. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 100965194

Pre-processing Agilent microarray data. Keywords Mesh Terms:

KEYWORDS: Oligonucleotide Array Sequence Analysis

MESH TERMS: statistics & numerical data

Chemical & Substance for Abstract: Pre-processing Agilent microarray data. Information

Substance Name:

Registry Number:

Grant and Affiliation Information for Pre-processing Agilent microarray data.

AFFILIATION: Johns Hopkins University School of Medicine, Oncology Biostatistics, Baltimore, MD 21205, USA. zahurma@jhmi.edu

Country: England

AGENCY: United States NCI

GRANT: P30 CA06973-44

ACRONYM: CA

MEDLINETA: BMC Bioinformatics

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Pre-processing Agilent microarray data Related Publications

• A GENERALIZED THEORY OF PARTICULATE ELECTRON CONDUCTION ENZYMES APPLIED TO CYTOCHROME OXIDASE. A THEORY OF COUPLED ELECTRON AND/ OR ION TRANSPORT APPLIED TO PYRUVATE CARBOXYLASE. NADC-ML-6405.
• A method for digital calculation of absolute free radical concentrations. NADC-MR-6804.
• A theory of cell hydration predicated on adsorption of water on cell proteins. NADA-NR-6701.
• Actinomycosis involving the colon and the rectum.
• Actinomycosis of bone with special reference to infection of vertebral column.
• Anatomy of the sacral venous plexus.
• Balloon dilatation of closed mesocaval shunts.
• Conversion from small (0.018 inch) to large (0.038 inch) guide wires in percutaneous drainage procedures.
• Diagnosis of sacral neoplasms by epidural venography.
• Directable cannula for gastrojejunal catheterization.
• Effects of level and frequency on the audibility of partials in inharmonic complex tones.
• Empirically derived combinations of tools and clinical cutoffs: an illustrative case with a sample of culturally/linguistically diverse children.
• Endoscopic replacement of drain catheters.
• Enhanced transmission at a spinal synapse triggered in vivo by an injury signal independent of altered synaptic activity.
• Environmental fate of chlorothalonil in a Costa Rican banana plantation.
• Improved anchoring of nephrostomy catheters: loop technique.
• Improved catheter introducer with recessed sheath.
• Literary surgeons.
• Low-temperature embedding in water-miscible methacrylates after treatment with antifreezes.
• Optical properties of highly scattering media determined from changes in attenuation, phase, and modulation depth.
• Percutaneous subhepatic cholecystostomy with removable anchor.
• Percutaneous treatment of superior vena cava syndrome.
• Pre-processing Agilent microarray data.
• Replacement of obstructed loop and pigtail nephrostomy and biliary drains.
• Simple technique for redirecting malpositioned central venous catheters.
• Suture anchor for visceral drainage.
• The effect of some insecticides on black fly larvae in Alaskan streams.
• Use of crossed-limb loop anchor for percutaneous biliary bypass.
• Usefulness of a percutaneous transhepatic coaxial micropuncture needle technique in patients with nondilated peripheral intrahepatic ducts.
• [Not Available.]