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The aim of this paper is to study in detail on a large number of experiments the behavior of the average PM\/MM ratio. This is taken as an indicator of the quality of the hybridization and, when compared between different chip series, of the quality of the chip design.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>About 250 different GeneChip hybridizations performed at the VIB Microarray Facility for <jats:italic>Homo sapiens<\/jats:italic>, <jats:italic>Drosophila melanogaster<\/jats:italic>, and <jats:italic>Arabidopsis thaliana<\/jats:italic> were analyzed. The investigation of such a large set of data from the same source minimizes systematic experimental variations that may arise from differences in protocols or from different laboratories. The PM\/MM ratios are derived theoretically from thermodynamic laws and a link is made with the sequence of PM and MM probe, more specifically with their central nucleotide triplets.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The PM\/MM ratios subdivided according to the different central nucleotides triplets follow qualitatively those deduced from the hybridization free energies in solution. It is shown also that the PM and MM histograms are related by a simple scale transformation, in agreement with what is to be expected from hybridization thermodynamics. Different quantitative behavior is observed on the different chip organisms analyzed, suggesting that some organism chips have superior probe design compared to others.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-3","type":"journal-article","created":{"date-parts":[[2009,1,6]],"date-time":"2009-01-06T19:13:11Z","timestamp":1231269191000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Thermodynamic scaling behavior in genechips"],"prefix":"10.1186","volume":"10","author":[{"given":"Alessandro","family":"Ferrantini","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joke","family":"Allemeersch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Van Hummelen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enrico","family":"Carlon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,1,6]]},"reference":[{"key":"2733_CR1","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1038\/4447","volume":"21","author":"RJ Lipshutz","year":"1999","unstructured":"Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ: High density synthetic oligonucleotide arrays. 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