Abstract
BackgroundThere are mechanisms, notably ozone degradation, that can damage a single channel of two-channel microarray experiments. Resulting analyses therefore often choose between the unacceptable inclusion of poor quality data or the unpalatable exclusion of some (possibly a lot of) good quality data along with the bad. Two such approaches would be a single channel analysis using some of the data from all of the arrays, and an analysis of all of the data, but only from unaffected arrays. In this paper we examine a 'combined' approach to the analysis of such affected experiments that uses all of the unaffected data.ResultsA simulation experiment shows that while a single channel analysis performs relatively well when the majority of arrays are affected, and excluding affected arrays performs relatively well when few arrays are affected (as would be expected in both cases), the combined approach out-performs both. There are benefits to actively estimating the key-parameter of the approach, but whether these compensate for the increased computational cost and complexity over just setting that parameter to take a fixed value is not clear. Inclusion of ozone-affected data results in poor performance, with a clear spatial effect in the damage being apparent.ConclusionThere is no need to exclude unaffected data in order to remove those which are damaged. The combined approach discussed here is shown to out-perform more usual approaches, although it seems that if the damage is limited to very few arrays, or extends to very nearly all, then the benefits will be limited. In other circumstances though, large improvements in performance can be achieved by adopting such an approach.
Highlights
There are mechanisms, notably ozone degradation, that can damage a single channel of two-channel microarray experiments
The advice from a producer of microarray systems [5] is either to avoid high ozone levels when conducting experiments, or to use one of a number of Cy5 stabilizing solutions that have been shown to prevent a good deal of the degradation
Most of the trends are as would be expected; the Single Channel analysis is consistent across the four levels of damage to the data and the other methods show a decline in performance as the percentage of damaged arrays increases
Summary
There are mechanisms, notably ozone degradation, that can damage a single channel of two-channel microarray experiments. Resulting analyses often choose between the unacceptable inclusion of poor quality data or the unpalatable exclusion of some (possibly a lot of) good quality data along with the bad Two such approaches would be a single channel analysis using some of the data from all of the arrays, and an analysis of all of the data, but only from unaffected arrays. BMC Bioinformatics 2007, 8:26 http://www.biomedcentral.com/1471-2105/8/26 that for two-channel microarray experiments, conducted without protection in a high-ozone environment, one channel of information may be partially or completely corrupted. While this relationship may not have been accepted universally [4], the fact that arrays with a defective Cy5 channel exist is not disputed. One can imagine circumstances where all of these approaches might suffice, one can see that there are drawbacks to each
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