Thanks steve. I figured out how to solve the 2and and 3rd problem, but I am
still unable to interpret the "under" concept with HyperGTest.  I can
interpret the result statistically but how you interpret that biologically?


On Mon, Nov 12, 2012 at 10:34 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Mon, Nov 12, 2012 at 9:30 AM, Mary Kindall <mary.kindall@gmail.com>
> wrote:
> >    1.
> >
> >    How do I interpret the result of 'hyperGTest' if the argument
> >    "testDirection='under'" is supplied? The hypergtest result is given
> below.
>
> Are you looking for help in interpreting this test in a statistical
> sense, or a biological one?
>
> >    2.
> >
> >    Is there a way to find all Entrez IDs associated with a particular GO
> >    term (For example, GO:0034660).
>
> Here is the "old school" way -- I bet there is now a nicer way to do
> this with the Homo.sapiens package (for instance). But let's say you
> wanted all human genes that are annotated with SMAD binding
> ("GO:0046332")
>
> R> library(org.Hs.eg.db)
> R> head(org.Hs.egGO2ALLEGS[["GO:0046332"]])
> R>   IDA   IDA   IDA   IDA   IDA   IDA
>  "90"  "91"  "94" "650" "657" "658"
>
> The names of the vector tell you the evidence code for the term ->
> gene association
>
> >    3.
> >
> >    How do I find list of all Entrez IDs which has a GO BP/CC/MF term? My
> >    gene universe 'uGenes' initially had a total of ~22,000 genes, where
> as the
> >    result below show it to be 19,703. This mean that some of my genes in
> the
> >    universe did not have an associated GO term. How to find those which
> were
> >    left out?
>
> Once you have your GO term of interest, this is essentially the same
> question (2), no?
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
-------------
Mary Kindall
Yorktown Heights, NY
USA

	[[alternative HTML version deleted]]

