User: Gilbert Feng
Gilbert Feng • 300
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Posts by Gilbert Feng
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Comment:
C: GeneAnswer package Query
... Can you run dim(getEnrichmentInfo(xx)) ? Because there is a warning
here, "Some specified categories might not be statistical significant!
Only show significant categories.". So if there is none significant
pathway based on geneAnswersBuilder, you can't get the network.
Gilbert
From: Reema Singh & ...
written 6.8 years ago by
Gilbert Feng • 300
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Answer:
A: GeneAnswer package Query
... Hi, Reema
Please give us more info, like Steve and Sean stated in their previous
responses.
Basically, for geneAnswersConceptNet(), xx should be an instance of
GeneAnswers. So you can run
> class(xx)
If the output is not like this,
[1] "GeneAnswers"
attr(,"package")
[1] "GeneAnswers"
You ne ...
written 6.8 years ago by
Gilbert Feng • 300
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... Hello,
I am using reactome.db for over-representive enrichment test, so I
wonder how I can get the total gene number for a given species in
reactome.db. For example, how many human genes (unique Entrez Ids) are
annotated in reactome.db? Is there any simple way to get this number
besides counting th ...
written 6.9 years ago by
Gilbert Feng • 300
• updated
6.8 years ago by
Marc Carlson • 7.2k
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... Hi, January
GeneAnswers integrates GO, DO, KEGG, and caBIO(NCI, Reactome and
Biocarta) as well as gene interaction and entrez keywords search for
gene set enrichment analysis. Finally, it can automatically generate a
html report for one or multiple groups of gene set enrichment analysis
with intera ...
written 8.3 years ago by
Gilbert Feng • 300
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Answer:
A: NCI pathways to graphNEL
... Hi, Laurent
Basically, GeneAnswers is designed for enrichment test based on
different annotation libraries. In your case, if you just want to
retrieve one or several NCI pathways, you can use standard xml query
to
obtain them from caBIO site. Then reconstruct the pathway by yourself
(GeneAnswers al ...
written 8.4 years ago by
Gilbert Feng • 300
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... Hi, Vincent
That's a good question. Currently, DO.obo file contains some synonyms
for each DO term/ID. Our collaborators are working on curation right
now. I'll talk to them about this. So far, what I can think is to
retrieve the synonyms from DO.obo and use some text mining tools to
find
the DO id ...
written 8.4 years ago by
Gilbert Feng • 300
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... Hi, Ted
Yes, your codes about mygenepool and mygenes are correct. I didn't
clearly state them in my previous email. Sorry about that. myDOLite
should be built by DOLite and mygenepool, not mygenes. So currently,
myDOLite is a customized annotation library and when you build a
geneAnswers instance, ...
written 8.4 years ago by
Gilbert Feng • 300
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... Hi, Ted
If I correctly understand your question, you have your own gene pool,
don't you? In that case, GeneAnswers still can handle that. What you
need is to build a customized DOLite list to run analysis. For
example,
if your genes are mygenes(an unique Entrez GENE ID vector)
myDOLite <- lapp ...
written 8.4 years ago by
Gilbert Feng • 300
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... Yes, Peter, that's true. The 1st version GeneAnswers has such
question,
but the current one has solved it. In geneAnswerBuilder, there is new
parameter, known(default is TRUE), which means only use annotated
genes
as the gene pool. There is another parameter,totalGeneNumber, for
customized annotatio ...
written 8.4 years ago by
Gilbert Feng • 300
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... Thanks, Peter. Yes, Fundo is also a good choice. It also uses
hypergeometric test, but it can show the GeneRef evidence for the
association between diseases and genes.
Gilbert
On 1/27/11 9:39 AM, Peter Robinson wrote:
> On 01/27/2011 04:17 PM, Gilbert Feng wrote:
>> Hi, Ted
>>
>& ...
written 8.4 years ago by
Gilbert Feng • 300
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