Identifying differential exon splicing using linear models and correlation coefficients |
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Authors: | Sonia H Shah and Jacqueline A Pallas |
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Institution: | (1) Bloomsbury Centre for Bioinformatics, Department of Computer Science, University College London, Gower Street, London, UK;(2) Wolfson Institute of Biomedical Research, University College London, Gower Street, London, UK |
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Abstract: | Background With the availability of the Affymetrix exon arrays a number of tools have been developed to enable the analysis. These however
can be expensive or have several pre-installation requirements. This led us to develop an analysis workflow for analysing
differential splicing using freely available software packages that are already being widely used for gene expression analysis.
The workflow uses the packages in the standard installation of R and Bioconductor (BiocLite) to identify differential splicing.
We use the splice index method with the LIMMA framework. The main drawback with this approach is that it relies on accurate
estimates of gene expression from the probe-level data. Methods such as RMA and PLIER may misestimate when a large proportion
of exons are spliced. We therefore present the novel concept of a gene correlation coefficient calculated using only the probeset
expression pattern within a gene. We show that genes with lower correlation coefficients are likely to be differentially spliced. |
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Keywords: | |
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