title: Reproducibility of gene expression across generations of Affymetrix microarrays.
abstract: BACKGROUND
  The development of large-scale gene expression profiling technologies is rapidly changing the norms of biological investigation. But the rapid pace of change itself presents challenges. Commercial microarrays are regularly modified to incorporate new genes and improved target sequences. Although the ability to compare datasets across generations is crucial for any long-term research project, to date no means to allow such comparisons have been developed. In this study the reproducibility of gene expression levels across two generations of Affymetrix GeneChips (HuGeneFL and HG-U95A) was measured.
  
  
  RESULTS
  Correlation coefficients were computed for gene expression values across chip generations based on different measures of similarity. Comparing the absolute calls assigned to the individual probe sets across the generations found them to be largely unchanged.
  
  
  CONCLUSIONS
  We show that experimental replicates are highly reproducible, but that reproducibility across generations depends on the degree of similarity of the probe sets and the expression level of the corresponding transcript.
authors.affiliation: Informatics Program, Children's Hospital, Harvard Medical School, Boston, MA, USA. ashish@chip.org
authors.forename: Ashish
authors.initials: A
authors.lastname: Nimgaonkar
authors.forename: Despina
authors.initials: D
authors.lastname: Sanoudou
authors.forename: Atul J
authors.initials: AJ
authors.lastname: Butte
authors.forename: Judith N
authors.initials: JN
authors.lastname: Haslett
authors.forename: Louis M
authors.initials: LM
authors.lastname: Kunkel
authors.forename: Alan H
authors.initials: AH
authors.lastname: Beggs
authors.forename: Isaac S
authors.initials: IS
authors.lastname: Kohane
mesh_terms: D002138:Calibration; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods / Q000592:standards / Q000706:statistics & numerical data; D018076:DNA, Complementary / Q000032:analysis / Q000235:genetics; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods* / Q000592:standards / Q000706:statistics & numerical data; D005786:Gene Expression Regulation / Q000235:genetics; D006801:Humans; D018482:Muscle, Skeletal / Q000737:chemistry / Q000166:cytology; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods* / Q000592:standards / Q000706:statistics & numerical data; D012313:RNA / Q000032:analysis / Q000235:genetics / Q000592:standards; D015347:RNA Probes / Q000235:genetics / Q000592:standards; D018075:RNA, Complementary / Q000032:analysis; D016008:Statistical Distributions
chemical_list: D018076:DNA, Complementary; D015347:RNA Probes; D018075:RNA, Complementary; D012313:RNA