Exact(4)
One microarray from the MAS98.06 model was removed due to poor array quality.
Furthermore, (v) the decision to filter out poor arrays can be made later, because a poor array will not affect the preprocessing of other arrays.
Ninety μg seemed to be the upper limit (more DNA resulted in poor array performance), and this corresponds to roughly 1 fmole haploid A. thaliana genomes and 267 amoles of haploid rice genomes.
While the outlier arrays detected by our method correspond to arrays that are outside the cluster of gene expression estimate PCA plots, our approach provides improved discriminatory power in that it permits discrimination of arrays that are outliers due to poor array quality compared with those that are likely to reflect actual biological variance.
Similar(56)
In bold, values indicating poor quality array.
Data was censored if more than one data value was flagged in each group to eliminate poor quality array data.
Of particular applicability to proteomics data are the ideas presented by Kauffmann et al. They note that a poor quality array will impede the statistical and biological significance of the analysis due to the added noise.
IQRray outperforms other methods in identification of poor quality arrays in datasets composed of arrays from many independent experiments.
This clearly demonstrates in two independent cohorts that the older an FFPE sample the poorer the array performance.
For RP analysis, samples matching the two poor quality arrays were removed as this analysis utilizes the ranked expression values from replicate samples.
Note that the performance of this algorithm may be influenced by poor quality arrays, especially those with highly scattered and unevenly distributed probe signal intensities.
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