Entering edit mode
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