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Open Access Methodology article

A model of binding on DNA microarrays: understanding the combined effect of probe synthesis failure, cross-hybridization, DNA fragmentation and other experimental details of affymetrix arrays

Yasminka A Jakubek12 and David J Cutler1*

Author Affiliations

1 Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA

2 Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA, 30322, USA

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BMC Genomics 2012, 13:737  doi:10.1186/1471-2164-13-737

Published: 27 December 2012

Additional files

Additional file 1:

Table 1A. Values for H are in J/mol. Values for S are in J/(K*mol).

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Additional file 2:

Figure 1. For each Forward/Reverse probe pair the mean of the log (Forward/Reverse) was calculated across all 62 chips from the FMR1 design. Probes are binned by base composition with each bin corresponding to the excess of A over T nucleotides plus the excess of C over G nucleotides on the Forward strand. The numbers on the figure correspond to the number of distinct features that are observed in the bin. Observed (o) and expected means (*) are plotted for each bin.

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