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Review
. 2008 Feb;4(2):e6.
doi: 10.1371/journal.pcbi.0040006.

Comprehensive analysis of affymetrix exon arrays using BioConductor

Michał J Okoniewski  1 , Crispin J Miller
Affiliations
Review

Comprehensive analysis of affymetrix exon arrays using BioConductor

Michał J Okoniewski et al. PLoS Comput Biol. 2008 Feb.
No abstract available

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Conflict of interest statement

Competing interests. The authors have declared that there are no competing interests.

Figures

Figure 1
Figure 1. Differences in Array Design
On standard 3′IVT, arrays such as the HGU133plus2 chip, each gene is typically targeted by a single probeset placed at the 3′ end of the transcript. These probesets consist of 11 Perfect Match spots and 11 paired Mis-Match spots in which the middle residue has been changed. Exon arrays have probesets placed against each exon along the length of the gene. Exon array probesets have no paired Mis-Match spots and four probes per probeset.
Figure 2
Figure 2. Exon Arrays Can Be Analysed Using Standard Approaches Developed for 3′IVT Arrays
A standard pipeline for array processing involves 1. normalizing the arrays, 2. generating expression summaries, 3. filtering on correlation, fold-change, and/or statistical significance to select interesting probesets, 4. mapping those probesets to their target transcripts by annotation, and 5. visualization and downstream analysis.
Figure 3
Figure 3. Expression for STARD10, Mapped to Known Isoforms and Coloured According to Fold Change between MCF7 and MCF10A
Figure 4
Figure 4. 20 Differentially Expressed Genes Selected for High Variance within Their Probesets
Each row corresponds to a gene, each rectangle to an exon. Exons are arranged in sequence order. If an exon is targeted by multiple probesets, these are stacked vertically within that exon. The plot is coloured by fold change between MCF7 and MCF10A (red, up in MCF7; blue, up in MCF10A).
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