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GeneBASE (Gene-level Background Adjusted Selected probe Expression) is a strategy for estimating gene expression on Affymetrix exon arrays. The method includes a probe-specific background correction and a probe selection strategy in which a subset of probes with highly correlated intensities across multiple samples are chosen to summarize gene exprssion. An extension of the method, GeneBASE-xhyb applies a correction for cross-hybridization biases of gene-level expression.
| Output gene-level expression indexes | Instructions |
| Output background-corrected probe intensities | Instructions |
| Output correlations between probes and off-target transcripts | Instructions |
| Output presence/absence calls | Instructions |
| GSL - GNU Scientific Library |
| The C Clustering Library by Michiel Jan Laurens de Hoon |
This software is licensed under the GNU General Public License (GPL).
| Kapur, K., Jiang, H., Xing, Y. and Wong, W.H. Cross-hybridization modeling on Affymetrix exon arrays. Submitted, 2008. |
| Kapur, K., Xing, Y., Ouyang, Z. and Wong, W.H. Exon array assessment of gene expression. Genome Biology, 2007 8(5). |
| Xing, Y., Kapur, K. and Wong, W.H. Probe selection and expression index computation of affymetrix exon arrays. PLoS ONE, 2006, 1(1). |