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1.  Mathematical Biology in Biology Direct 
Biology Direct  2008;3:1.
doi:10.1186/1745-6150-3-1
PMCID: PMC2216004  PMID: 18199327
2.  Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis? 
Biology Direct  2007;2:28.
Background.
This work was undertaken in response to a recently published paper by Okoniewski and Miller (BMC Bioinformatics 2006, 7: Article 276). The authors of that paper came to the conclusion that the process of multiple targeting in short oligonucleotide microarrays induces spurious correlations and this effect may deteriorate the inference on correlation coefficients. The design of their study and supporting simulations cast serious doubt upon the validity of this conclusion. The work by Okoniewski and Miller drove us to revisit the issue by means of experimentation with biological data and probabilistic modeling of cross-hybridization effects.
Results.
We have identified two serious flaws in the study by Okoniewski and Miller: (1) The data used in their paper are not amenable to correlation analysis; (2) The proposed simulation model is inadequate for studying the effects of cross-hybridization. Using two other data sets, we have shown that removing multiply targeted probe sets does not lead to a shift in the histogram of sample correlation coefficients towards smaller values. A more realistic approach to mathematical modeling of cross-hybridization demonstrates that this process is by far more complex than the simplistic model considered by the authors. A diversity of correlation effects (such as the induction of positive or negative correlations) caused by cross-hybridization can be expected in theory but there are natural limitations on the ability to provide quantitative insights into such effects due to the fact that they are not directly observable.
Conclusion.
The proposed stochastic model is instrumental in studying general regularities in hybridization interaction between probe sets in microarray data. As the problem stands now, there is no compelling reason to believe that multiple targeting causes a large-scale effect on the correlation structure of Affymetrix gene expression data. Our analysis suggests that the observed long-range correlations in microarray data are of a biological nature rather than a technological flaw.
Reviewers:
The paper was reviewed by I. K. Jordan, D. P. Gaile (nominated by E. Koonin), and W. Huber (nominated by S. Dudoit).
doi:10.1186/1745-6150-2-28
PMCID: PMC2211459  PMID: 17988401
3.  How high is the level of technical noise in microarray data? 
Biology Direct  2007;2:9.
Background
Microarray gene expression data are commonly perceived as being extremely noisy because of many imperfections inherent in the current technology. A recent study conducted by the MicroArray Quality Control (MAQC) Consortium and published in Nature Biotechnology provides a unique opportunity to probe into the true level of technical noise in such data.
Results
In the present report, the MAQC study is reanalyzed in order to quantitatively assess measurement errors inherent in high-density oligonucleotide array technology (Affymetrix platform). The level of noise is directly estimated from technical replicates of gene expression measurements in the absence of biological variability. For each probe set, the magnitude of random fluctuations across technical replicates is characterized by the standard deviation of the corresponding log-expression signal. The resultant standard deviations appear to be uniformly small and symmetrically distributed across probe sets. The observed noise level does not cause any tangible bias in estimated pair-wise correlation coefficients, the latter being particularly prone to its presence in microarray data.
Conclusion
The reported analysis strongly suggests that, contrary to popular belief, the random fluctuations of gene expression signals caused by technical noise are quite low and the effect of such fluctuations on the results of statistical inference from Affymetrix GeneChip microarray data is negligibly small.
Reviewers
The paper was reviewed by A. Mushegian, K. Jordan, and E. Koonin.
doi:10.1186/1745-6150-2-9
PMCID: PMC1855048  PMID: 17428341

Results 1-3 (3)