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This package provides a collection of techniques to remove inter-study bias when combining gene expression data originating from different studies.
● Data Source:
BioConductor
● Keywords:
● Alias: inSilicoMerging, inSilicoMerging-package
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merge
(Package: inSilicoMerging) :
General method to merge different ExpressionSets
General method to merge different ExpressionSets by applying different techniques to remove inter-study bias.
● Data Source:
BioConductor
● Keywords:
● Alias: merge
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Gene-wise boxplots describe the gene-wise distribution of samples. Sample can be grouped together using the batchLabel parameter and can be coloroed usig the colLabel parameter for optimal visualization of the possible batch effects.
● Data Source:
BioConductor
● Keywords:
● Alias: plotGeneWiseBoxPlot
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plotMDS
(Package: inSilicoMerging) :
Create double-labeled MDS plot from (merged) ExpressionSet
Create Multidimensional Scaling (MDS) plot from ExpressionSet. Very similar to Principal Component Analysis (PCA) plots all samples are plotted in a two-dimensional space where both axis represent the two principle axis of expression variation. In this plot each sample can be labeled with a color and with a symbol.
● Data Source:
BioConductor
● Keywords:
● Alias: plotMDS
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plotRLE
(Package: inSilicoMerging) :
Create RLE plot from (merged) ExpressionSet
Create relative log expression (RLE) plot from ExpressionSet. RLE plots were initially proposed to measure the overall quality of a dataset but can also be used to visualize the presence of unwanted batch effects in the data.
● Data Source:
BioConductor
● Keywords:
● Alias: plotRLE
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