| Main Title |
Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays / |
| Author |
Yuen, Tony .
|
| Other Authors |
|
| Publisher |
Oxford University Press, [University of Illinois Graduate School of Library Science], |
| Year Published |
2002 |
| OCLC Number |
1428796486 |
| Subjects |
DNA microarrays ;
Oligonucleotides
|
| Holdings |
| Library |
Call Number |
Additional Info |
Location |
Last
Modified |
Checkout
Status |
| ELBM |
QP625.O47Y84 2002 |
|
AWBERC Library/Cincinnati,OH |
04/10/2024 |
|
| Collation |
9 pages : illustrations ; 28 cm |
| Notes |
Offprint: Nucleic Acids Research. Volume 30, no. 10 e48 (May 15, 2002) Includes bibliographical references (page 9) |
| Contents Notes |
We compared the accuracy of microarray measurements obtained with oligonucleotide arrays (GeneChip, Affymetrix) with a laboratory-developed cDNA array by assaying test RNA samples from an experiment using a paradigm known to regulate many genes measured on both arrays. We selected 47 genes represented on both arrays, including both known regulated and unregulated transcripts, and established reference relative expression measurements for these genes in the test RNA samples using quantitative reverse transcriptase real-time PCR (QRTPCR) assays. The validity of the reproducible (average coefficient of variation = 11.8%) QRTPCR measurements were established through application of a new mathematical model. The performance of both array platforms in identifying regulated and non-regulated genes was identical. With either platform, 16 of 17 definitely regulated genes were correctly identified, and no definitely unregulated transcript was falsely identified as regulated. Accuracy of the fold-change measurements obtained with each platform was assessed by determining measurement bias. Both platforms consistently underestimate the relative changes in mRNA expression between experimental and control samples. The bias observed with cDNA arrays was predictable for fold-changes <250-fold by QRTPCR and could be corrected by the calibration function Fc = Fa(cDNA)q, where Fa(cDNA) is the microarray-determined fold-change comparing experimental with control samples, q is the correction factor and Fc is the calibrated value. The bias observed with the commercial oligonucleotide arrays was less predictable and calibration was unfeasible. Following calibration, fold-change measurements generated by custom cDNA arrays were more accurate than those obtained by commercial oligonucleotide arrays. Our study demonstrates systematic bias of microarray measurements and identifies a calibration function that improves the accuracy of cDNA array data. |
| Place Published |
Urbana, Ill. |
| Access Notes |
Available online |
| PUB Date Free Form |
1975 |
| BIB Level |
m |
| Medium |
unmediated |
| Content |
text |
| Carrier |
volume |
| Cataloging Source |
OCLC/T |
| OCLC Time Stamp |
20240405213018 |
| Language |
eng |
| Origin |
OCLC |
| Type |
CAT |
| OCLC Rec Leader |
03455nam 2200385 a 45010 |
