Linked Life Data

12000853

Source:http://linkedlifedata.com/resource/pubmed/id/12000853

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
10
pubmed:dateCreated
2002-5-9
pubmed:abstractText
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 F(c) = F(a(cDNA))(q), where F(a(cDNA)) is the microarray-determined fold-change comparing experimental with control samples, q is the correction factor and F(c) 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.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-10328870, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-10521349, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-10676951, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-11161795, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-11292855, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-11328886, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-11665639, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-9872747, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-9894600, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-9915496, http://linkedlifedata.com/resource/pubmed/commentcorrection/12000853-9915498
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
May
pubmed:issn
1362-4962
pubmed:author
pubmed:issnType
Electronic
pubmed:day
15
pubmed:volume
30
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
e48
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2002
pubmed:articleTitle
Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays.
pubmed:affiliation
Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't