The Golden Spike: Technical Comments

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Irizarry and colleagues explain why it might be difficult to use the Choe et al. data with their Affycomp benchmark evaluations in a Correspondence in Genome Biology. Their paper raises some interesting questions about the assumptions typically made during microarray normalization and analysis. Our response to their comments can be found here.

Alan Dabney and John Storey have pointed out that problems with FDR estimates in the Choe et al. paper stem from earlier problems with p-value distributions. This may explain why the FDR estimates were too low. They also argue that the distribution issues are caused by a flawed experimental design. See their comments and why we disagree with the latter point here. Read a more detailed treatment of our new analysis of normalization issues here and here. Fodor et al. show that non-uniform p-value distributions may be a common issue in microarray analysis and suggest some fixes in this Genome Biology paper.

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