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We consider the merged data set: K = [ K1, K2,..., K J ], where each K j corresponds to an 'Omics' data table.
A recent analysis of a high confidence merged data set representing 12 independent HTP studies, called the 12 HQ data set, suggested that the yeast phosphoproteome is gradually approaching saturation because the average overlap of phosphosites between any two experiments is 12%, whereas the overlap between phosphoproteins in total is 28% (35).
Data from all congenics was merged and the analysis was carried out in the merged data set.
As can be seen, ComBat was successful in removing dataset-specific biases (Figure 2, Figure 3) since the samples of the merged data set integrated with ComBat were better intermixed than the samples merged with Z-score normalization.
As an individual gene may have limited instances for a particular category, we merged classification results from the top eight genes and reported category-specific performance on the merged data set.
If this were not the case, then the gene would not be present in the merged data set, which could explain the rather disappointing prediction accuracy figures obtained after merging.
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We use survival prediction based on Cox regression as an assay to measure the added value of merged data sets.
Taken all these together, however, the improvement seen with selectively merged data sets is relatively modest as compared to the prognostic power generated from the merged data sets composed of all OS single data sets.
(4) The merged data sets' hypervariable regions were then hand curated using splicer, a tool we developed and made available on the Web as part of our pipeline TORNADO at http://tornado.igb.uiuc.edu/.igb.uiuc.edu/
In most studies, the concordance between the merged data sets and their interpretation in the context of biological pathways and regulatory mechanisms are investigated.
"This means making it easy for the people to upload, to merge data sets, to discuss the data, to create visualizations and then to take these visualizations and put them elsewhere on the Web".
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