Detailed descriptions of the various analysis methods of the Bioconductor packages and their usage are described in the so called package vignettes.
The links to the package vignettes of the Bioconductor packages used in CARMAweb are available below.
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Description of Bioconductors affy package used for the preprocessing of Affymetrix GeneChips
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Visualizations of GO (GOstats package)
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Gene Ontology (GO) analysis and statistical issues in GO analysis (GOstats package)
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Preprocessing of two color microarrays and linear models in microarray analysis (limma package). Detection of differentially expressed genes using moderated t-statistics.
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Description of the various Affymetrix preprocessing methods
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Variance stabilizing normalization
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Multiple hypothesis testing in microarray experiments. Adjustment methods for multiple hypothesis testing (multtest package)
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Description of the gcrma Affymetrix preprocessing method
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Significance analysis of microarray data (SAM, siggenes package)
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