Using Bioconductor To Analyse Beadarray Data: Difference between revisions
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ebFit = eBayes(fit.cont) | ebFit = eBayes(fit.cont) | ||
</pre> | </pre> | ||
===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 | |||
***method | |||
****default is "global", which allows for p-value comparasons | |||
***adjust.method, this defines the false-discovery rate adjustment: | |||
****default is "BH" for Benjami and Hochberg | |||
****other options are "none", "fdr" (same as BH), "holm" and "BY" | |||
==Annotation of Expression Sets and Fitted Data== | |||