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Old 07-05-2014, 03:36 AM   #6
blancha
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Location: Montreal

Join Date: May 2013
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There are also several ways of analyzing the biological significance of the data.

goseq: R package to do gene ontology analysis. Corrects for length bias in RNA-Seq. Cumbersome to use. Default output not complete, e.g. ontology terms but not the genes inputted that are associated with the terms.

DAVID: Very easy to use. Biologists can do it. Does not correct for length bias. Algorithm rather mysterious. Interactive and informative output. Very easy to play with.

GSEA: Different algorithm. Can pick gene sets. Criteria must be chosen to rank genes however. There is no perfect ranking. Ranking by fold changes or adjusted p-values both have their disadvantages.
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