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Used internally by processExpressionSet. Code to either take the average across a set of duplicated "keys" (can be probes or genes, which correspond to the rows in the expression matrix "expr"), or take the keys that has the highest variance across the set of duplicated keys.
● Data Source:
BioConductor
● Keywords:
● Alias: collapseDupProbes
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34 manually curated high-quality gene expression microarray datasets with advanced beast cancer samples collected from GEO. All datasets provided have some form of survival and treatment information, and all such clinical variables are semantically normalized across all datasest for easy analyses across datasets. Authors of the Pubmed article linked to each GEO dataset was contacted in an effort to collect as much extra clinical data as possible. See vignette and publication reference from AMIA Translational Science Joint Summits presentation in 2013 for more details on how this data was curated.
● Data Source:
BioConductor
● Keywords: package
● Alias: curatedBreastData, curatedBreastData-package
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A method that removes samples or genes with high NA rates and then KNN imputes remaining missing values.
● Data Source:
BioConductor
● Keywords:
● Alias: filterAndImputeSamples
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A function that filters genes by variance; it can simply threshold out genes that are above or below a certain magnitude of variance, filter out genes that fall outside of a minimum and maximum percentile, or simply select the top N varying genes.
● Data Source:
BioConductor
● Keywords:
● Alias: filterGenesByVariance
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This function Post-processes a normalized assayData in an ExpressionSet object. Is is assumed the assay data is already baseline normalized (for example, for microarray data, this could mean quantile normalized and then logged.)
● Data Source:
BioConductor
● Keywords:
● Alias: processExpressionSet
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A wrapper function for the post-processing function processExpressionSet() on a list of S4 expressionSet objects. This function is run after initial dataset normalization, such as quantile normalization on microarray datasets.
● Data Source:
BioConductor
● Keywords:
● Alias: processExpressionSetList
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Function to keep only 1 sample per patient (column ID) in the data matrix. Keeps the sample that has the overall highest variance.
● Data Source:
BioConductor
● Keywords:
● Alias: removeDuplicatedPatients
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providing 
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