Package 'virtualArray' - Bioconductor

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14 virtualArrayComBat Examples ## first we need to load dummy data library(affydata) data(Dilution) data(sample.ExpressionSet) ## we apply RMA to get an ExpressionSet Dilution
virtualArrayCompile 15 Value Returns a matrix holding adjusted expression values. Note Original code by Johnson, WE, Rabinovic, A, and Li, C, made available in this package by Andreas Heider Author(s) Original author: Johnson, WE, Rabinovic, A, and Li, C (2007) Modified by: Andreas Heider (2011) References Johnson, WE, Rabinovic, A, and Li, C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118-127. See Also virtualArray-package, virtualArray.ExpressionSet, virtualArrayCompile Examples ## EMPTY virtualArrayCompile Compiles a single virtual array holding user provided microarray data from multiple platforms. Description The function takes ExpressionSets of rawdata provided by the "virtualArrayLoadRaw" function together with annotation data.frames provided by the function "virtualArray.load.annot" and matches the rawdata on the basis of the given identifier. Currently only "Gene.Symbol" is supported by "virtualArrayCompile" but this will be extendend in future versions. Meanwhile you can use "virtualArray.ExpressionSet" to use other identifiers. Usage virtualArrayCompile(root_dir = getwd(), identifier = "Gene.Symbol", covars= 3, virtualArray = virtualAr
Page 1 and 2: Package ‘virtualArray’ October
Page 3 and 4: virtualArray-package 3 meta-analysi
Page 5 and 6: normalize.ExpressionSet.gq 5 normal
Page 7 and 8: normalize.ExpressionSet.mrs 7 See A
Page 9 and 10: normalize.ExpressionSet.qd 9 Refere
Page 11 and 12: virtualArrayBuildExprs 11 virtualAr
Page 13: virtualArrayBuildSampleInfo 13 Exam
Page 17 and 18: virtualArrayExpressionSets 17 Usage
Page 19 and 20: virtualArrayHclust 19 sample_info d
Page 21 and 22: virtualArrayMergeRecurse 21 Usage v
Page 23 and 24: Index ∗Topic ExpressionSet virtua

Package 'virtualArray' - Bioconductor

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