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Using Bioconductor To Analyse Beadarray Data

221 bytes added, 17:56, 21 August 2009
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→‎Generating a Venn Diagram for Differential Expression
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===Generating a Venn Diagram for Differential Expression===
*First define a cutoff criteria for inclusion.# One option is to use the decideTests function:
<pre>results = decideTests(ebFit, method="global")</pre>
*The relevant options are for method and adjust.method
***default is "BH" for Benjami and Hochberg
***other options are "none", "fdr" (same as BH), "holm" and "BY"
#*Now use that classification to generate the Venn Diagram. The following will include both up and downregulated genes and color the numbers accordingly:<pre>vennDiagram(results, include="both", col=c("red","green")</pre>
==Annotation of Expression Sets and Fitted Data==