Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips® | Zendy

Kathe E. Bjork | Zendy; Karen Kafadar | Zendy

Open Access

Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips®

Author(s) -

Kathe E. Bjork,

Karen Kafadar

Publication year - 2007

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btm450

Subject(s) - automatic summarization , gene expression profiling , cluster analysis , computer science , profiling (computer programming) , gene chip analysis , expression (computer science) , computational biology , gene expression , data mining , dna microarray , biology , bioinformatics , gene , genetics , artificial intelligence , programming language , operating system

Affymetrix GeneChips are common 3' profiling platforms for quantifying gene expression. Using publicly available datasets of expression profiles from human and mouse experiments, we sought to characterize features of GeneChip data to better compare and evaluate analyses for differential expression, regulation and clustering. We uncovered an unexpected order dependence in expression data that holds across a variety of chips in both human and mouse data.

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