title: Are data from different gene expression microarray platforms comparable?
abstract: Many commercial and custom-made microarray formats are routinely used for large-scale gene expression surveys. Here, we sought to determine the level of concordance between microarray platforms by analyzing breast cancer cell lines with in situ synthesized oligonucleotide arrays (Affymetrix HG-U95v2), commercial cDNA microarrays (Agilent Human 1 cDNA), and custom-made cDNA microarrays from a sequence-validated 13K cDNA library. Gene expression data from the commercial platforms showed good correlations across the experiments (r = 0.78-0.86), whereas the correlations between the custom-made and either of the two commercial platforms were lower (r = 0.62-0.76). Discrepant findings were due to clone errors on the custom-made microarrays, old annotations, or unknown causes. Even within platform, there can be several ways to analyze data that may influence the correlation between platforms. Our results indicate that combining data from different microarray platforms is not straightforward. Variability of the data represents a challenge for developing future diagnostic applications of microarrays.
authors.affiliation: Biomedicum Biochip Center, University of Helsinki, P.O. Box 63, Room A415b, 00014 University of Helsinki, Finland.
authors.forename: Anna-Kaarina
authors.initials: AK
authors.lastname: Järvinen
authors.forename: Sampsa
authors.initials: S
authors.lastname: Hautaniemi
authors.forename: Henrik
authors.initials: H
authors.lastname: Edgren
authors.forename: Petri
authors.initials: P
authors.lastname: Auvinen
authors.forename: Janna
authors.initials: J
authors.lastname: Saarela
authors.forename: Olli-P
authors.initials: OP
authors.lastname: Kallioniemi
authors.forename: Outi
authors.initials: O
authors.lastname: Monni
mesh_terms: D045744:Cell Line, Tumor; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D015723:Gene Library; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D011786:Quality Control