[BioC] question using GSEABase

[Martin Morgan]

Hi Jiang,

Please keep posts on-list, so all can benefit (and clarify) our exchange.

topGO, GOstats, and PGSEA (forgot to mention that, sorry) all do 
variations of 'discrete' gene set analysis, comparing a list of 
'selected' genes with a 'universe' of genes. To use GOstats and topGO, 
you would need to augment your 'selected' genes (below) with a universe 
of genes; how you specify the universe has been covered on this mailing 
list before; it is often a subset of the genes represented on the array 
you've used to identify interesting genes.

I do not have an easy answer for how to start a Category analysis.
The analysis outlined in the Category vignette requires in addition the 
expression values, or at least relevant t-statistics, summarizing the 
differential expression that you are interested in. The vignette is not 
a 'recipe' that you can follow line-by-line, but rather an outline of 
the conceptual steps that can be taken. The essence of the approach 
begins on p. 3, where a matrix of expression values is assessed for 
differential expression, probes are mapped to pathways, and differential 
expression is summarized per-path.

Both types of analysis require some level of understanding of how 
Biocondcutor works.

Martin

chunjiang he wrote:
> I have a gene id list like:
> 27
> 97
> 104
> 273
> 287
> 355
> 361
> 382
> 387
> 411
> 517
> 538
> 577
>  
> or gene symbol list like:
> C9orf152
> FSTL1
> CREB3L1
> PNMA1
> RIT2
> SLC18A1
> CD44
> PCDHB15
> FARP1
> TMEM216
> KCNMA1
> C10orf90
> C9orf39
> ZHX3
> TUBD1
> 
> And if I want to start the Category analysis, how could I do. I see the 
> introduction of Category, but it is based on ALL data. So how could I 
> start with my data.
> Thanks very much
>  
> Best,
> Jiang
> On Fri, May 22, 2009 at 11:12 AM, chunjiang he <camelbbs at gmail.com 
> <mailto:camelbbs at gmail.com>> wrote:
> 
>     Thanks so much.
>     And does the result of Category is similar to GOstats or topGO. 
>     I want to know if there is need to use Category for my work.
>     Best,
>     Jiang
> 
>     On Fri, May 22, 2009 at 10:38 AM, Martin Morgan <mtmorgan at fhcrc.org
>     <mailto:mtmorgan at fhcrc.org>> wrote:
> 
>         chunjiang he wrote:
> 
>             hi all,
>             I have used GOstats and topGO to get the GO anotations of my
>             Gene list. Now
>             I hear about GSEABase can do more things about pathway
>             analysis. I installed
>             the GSEABase packages and study it. But I think I can't get
>             the pathway
> 
> 
>         GSEABase provides classes for organizing gene sets, and for
>         accessing gene sets available in other locations (such as those
>         at the Broad). It does not provide gene set analysis
>         functionality. In addition to GOstats and topGO, there is also
>         the Biocondcutor package Category, and third party tools.
> 
>         Martin
> 
>             analysis tools in GSEABase. And what is the result of GSEA
>             pathway analysis.
>             Anyone can help me.
>             Best,
>             Chunjiang
> 
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> 
> 
>         -- 
>         Martin Morgan
>         Computational Biology / Fred Hutchinson Cancer Research Center
>         1100 Fairview Ave. N.
>         PO Box 19024 Seattle, WA 98109
> 
>         Location: Arnold Building M1 B861
>         Phone: (206) 667-2793
> 
> 
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793