[BioC] Can any one please help me regadrding Illumina humanv3.microarray

[Steve Lianoglou]

Hi Pradeep,

(Please keep all correspondence on list by using "reply-all" when
replying to bioc-help messages)

On Mon, Nov 8, 2010 at 11:38 AM, Pradeep Battula <prabat at utu.fi> wrote:
> Dear Steve,
>
> Thanks a lot for your suggestion. and I also want to know, whether I have to perform all those Non-specific filtering tests, for the gene universe....Thanks in advance.

I'm sorry, I don't follow ... what non-specific filtering tests to the
gene universe are you referring to?

-steve

>
> Regards,
> Pradee.
>
> ----- Original Message -----
> From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
> Date: Monday, November 8, 2010 5:55 pm
> Subject: Re: [BioC] Can any one please help me regadrding Illumina humanv3.microarray
> To: Pradeep Battula <prabat at utu.fi>
> Cc: bioconductor at stat.math.ethz.ch
>
>
>> Hi,
>>
>> On Mon, Nov 8, 2010 at 10:44 AM, Pradeep Battula <prabat at utu.fi> wrote:
>> > Dear All,
>> >
>> > I want to write a function that performs hypergeometric test for
>> over representation against GO and KEGG, for the available example of
>> data of
>> > background.Datat: Entrez identifiers of all probes present on
>> Illumina human HT12 v3. microarray
>> > DEgenes.Data: Differentially expressed genes in a real study carried
>> out on Illumina HT12 v3. microarray
>> >
>> > But, the relevant documentation provided in "GOstats" and "topGO"
>> are explained using a microarray data set  from a clinical trial in
>> acute lymphoblastic leukemia (ALL).
>> >
>> > Now I want to know, can I apply the same documentation to my
>> available data or there any minor changes I have to make.
>>
>> If both your background.Data and DEgenes.Data are simply vectors of
>> entrez id's, then this is pretty straightforward. With GOstats, you
>> can do:
>>
>> R>   params <- new("GOHyperGParams", geneIds=DEgenes.data,
>>                 universeGeneIds=background.Data, annotation='org.Hs.eg.db',
>>                 ontology='BP', ...)
>> R> go.bp <- hyperGTest(params)
>>
>> -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
>



-- 
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