Open Access Highly Accessed Research article

Empirical bayes analysis of sequencing-based transcriptional profiling without replicates

Zhijin Wu1*, Bethany D Jenkins23, Tatiana A Rynearson3, Sonya T Dyhrman4, Mak A Saito5, Melissa Mercier3 and LeAnn P Whitney2

Author Affiliations

1 Center for Statistical Sciences and Department of Community Health, Box G-121S-7, Brown University, Providence RI 02912, USA

2 Department of Cell and Molecular Biology The University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA

3 The Graduate School of Oceanography, University of Rhode Island, South Ferry Road, Narragansett, RI 02882, USA

4 Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA 02543, USA

5 Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, 360 Woods Hole Rd, Woods Hole MA 02543, USA

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BMC Bioinformatics 2010, 11:564  doi:10.1186/1471-2105-11-564

Published: 16 November 2010

Additional files

Additional file 1:

Figure S1. A. Scatter plot of the log10 rpm in the A and B samples. Differentially expressed genes identified by DGEseq with estimated q-value (Storey FDR) less than 0.01 highlighted in red and the genes with smallest q-value 1000 of which highlighted in blue. B. Distribution of average rpm for the highlighted red or blue genes.

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Additional file 2:

Figure S2. Histogram of the apparent fold change of the top 1000 genes found by DGEseq or ASC.

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Additional file 3:

Figure S3. Sensitivity of <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M20','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M20">View MathML</a> to hyper-parameter estimation. Scatter plot of <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M21','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M21">View MathML</a> and <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M21','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M21">View MathML</a>, based on q1 = 0.8, q2 = 0.9 and q1 = .9, q2 = 0.95, respectively. The maximum difference in estimated fold change is less than 0.04, indicating that <a onClick="popup('http://www.biomedcentral.com/1471-2105/11/564/mathml/M20','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/11/564/mathml/M20">View MathML</a> is not sensitive to the choice of q.

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