question on ChIPpeakAnno::getEnrichedGO
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 4 months ago
United States
Cam, Thanks for the feedback and your kind word! Please see my response below. BTW, could you please cc the Bioconductor list bioconductor at r-project.org next time so that others could contribute or/and benefit? Thanks! Best regards, Julie On 8/28/13 1:29 PM, "Camila Lopez-anido" <lopezanido at="" wisc.edu=""> wrote: > Hi again,? > > Thanks for putting together the ChIPpeakAnno package! It's been really nice to > use. > > 1. I have a question about getEnrichedGO. I was wondering what you would > recommend to make the test more relaxed? Currently, I'm using maxP=0.05, > multiAdj=TRUE, minGOterm = 1, multiAdjMethod="BH". Should I not run multiAdj, > or use another multiAdjMethod? I usually use maxP = 0.05, multiAdj=TRUE, minGOterm = 5, multiAdjMethod="BH" You could try to set maxP = 0.1 and see if there are some terms with adjusted p-values on the boarder line. > > 2. Also, I wanted to check to see if getEnrichedGO filters the list of genes > prior to analysis?.... since more than 1 peak can be associated with the same > gene, which means that the same gene may be counted twice or more. Do > researchers usually use that data as is (i.e. multiples of the same gene), or > do they filter for a unique list prior to GO analyses? Very good question. Yes, the gene list is filtered to contain a unique gene list prior to GO anlayis. > > Thanks, > Cam
GO ChIPpeakAnno GO ChIPpeakAnno • 836 views
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