## Chunk 1
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library("Biobase")
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## Chunk 2
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data(ALL)
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## Chunk 5
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varCut = 0.5
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## Chunk 7
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hasSymbol = sapply(mget(featureNames(ALLfilt_bcrneg),
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## Chunk 8
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affyUniverse = featureNames(ALLfilt_bcrneg)
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## Chunk 10
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ttestCutoff = 0.05
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## Chunk 12
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## ## if you are following along with your own data...
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## Chunk 13
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hgCutoff = 0.001
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## Chunk 14
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hgOver = hyperGTest(params)
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## Chunk 15
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hgOver
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## Chunk 19
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htmlReport(hgOver, file="ALL_hgo.html")
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## Chunk 21
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sigSub = termGraphs(hgOver)
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## Chunk 23
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plotGOTermGraph(sigSub[[1]], hgOver, max.nchar=100)
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## Chunk 24
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paramsCond = params
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## Chunk 25
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hgCond = hyperGTest(paramsCond)
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## Chunk 26
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hgCond
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## Chunk 29
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terms = nodes(sigSub[[1]])
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