Hi Anna,

 

  I am sorry to not mention this before but by fold change I meant the following, fold change = ratio(treated with stimuli / non treated control). And for OMIM I have decided to create my own annotation package as that’s much easier to use.

 

Best Regards,

Chanchal 

===============================

Chanchal Kumar, Ph.D. Candidate

Dept. of Proteomics and Signal Transduction
Max Planck Institute of Biochemistry
Am Klopferspitz 18
82152 D-Martinsried (near Munich)
Germany
e-mail: chanchal@biochem.mpg.de <mailto:chanchal@biochem.mpg.de> 
Phone: (Office) +49 (0) 89 8578 2296

Fax:(Office) +49 (0) 89 8578 2219
http://www.biochem.mpg.de/mann/ <http://www.biochem.mpg.de/mann/> 
===============================

From: anna freni sterrantino [mailto:annafreni@yahoo.it] 
Sent: Friday, July 25, 2008 12:23 PM
To: Chanchal Kumar; bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?

 

I see what you mean, 
now that you mention the Broad Institute, 
as long I know, 
the pre-ranked list of genes is  ranked  to reflect differential  expressions
 between two classes, and not as in you case just by fold change values.
Any way  form Bioconductor, if you know at least the chip 
form where you got your EntrezID, you can easily  get 
OMIM, if it's available.


Good Luck

Anna




 ----- Messaggio originale -----

Da:Chanchal Kumar <chanchal@biochem.mpg.de>
A: anna freni sterrantino <annafreni@yahoo.it>; bioconductor@stat.math.ethz.ch
Inviato: Venerdì 25 luglio 2008, 11:43:26
Oggetto: RE: [BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?

Hi Anna,

 

  Thank you for the reply. As the GSEA(from Broad Institute) has an option for analyzing preranked list of genes so I was curious if similar functionality exists in Bioconductor as well. I will like to use GSEA to get the OMIM etc. related information using Bioconductor as I don’t think that’s available in the annotation packages. 

 

Best Regards,

Chanchal 

===============================

Chanchal Kumar,Ph.D. Candidate

Dept. of Proteomics and Signal Transduction
Max Planck Institute of Biochemistry
Am Klopferspitz 18
82152 D-Martinsried (near Munich)
Germany
e-mail: chanchal@biochem.mpg.de <mailto:chanchal@biochem.mpg.de> 
Phone: (Office) +49 (0) 89 8578 2296

Fax:(Office) +49 (0) 89 8578 2219
http://www.biochem.mpg.de/mann/ <http://www.biochem.mpg.de/mann/> 
===============================

From: anna freni sterrantino [mailto:annafreni@yahoo.it] 
Sent: Friday, July 25, 2008 11:03 AM
To: Chanchal Kumar; bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?

 

Hi  Chanchal ,
as long you  have only a list on entrezID, there is not much to do, oh well:
Of course you can get gene sets ,information related to the gene set structure, description etc 
it should be fine,  with GSEABase.

But to perform a Gene Set Enrichment Analysis, ( in a more  general framework) 
you'll  need  a statistic  ( usually a t-stat) at gene level 
and then you will use that  to compute a statistic for gene set level. 

As long as I understood from your email you only know the order
of gene's fold change, this kind of information is not enough, for this latter type of analysis.

Hope it helps

Best regards
Anna





 

----- Messaggio originale -----
Da: Chanchal Kumar <chanchal@biochem.mpg.de>
A: bioconductor@stat.math.ethz.ch
Inviato: Venerdì 25 luglio 2008, 1:14:20
Oggetto: [BioC] How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?

Dear All,

  I have a set of Entrez ids which have been ordered as per fold change
expression from a control experiment. I am now interested in carrying
out gene set enrichment analysis using Bioconductor GSEABase package. I
don't have any other statistics for these genes. Is it possible to carry
out GSEA on a vector of Entrezids which is ordered by say fold change? I
attach an example vector and would like to carry out GSEA on this test
set to get an idea of how this might work.

library(annotate)
library(hgu95av2.db)

set.seed(12345)
set1 <- unique(getEG(sample(ls(hgu95av2GO), 100), "hgu95av2"))
set1<-na.omit(set1) # as I get NAs in the vector before

For GSEA I assume that element set1[1] has highest fold change and
set1[length(set1)] has the lowest fold change. Any help in this regard
will be appreciated. Thanks in advance!

------------------------------------------------------------------------
---------------

> sessionInfo()
R version 2.7.0 (2008-04-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=
German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252

attached base packages:
[1] tools    stats    graphics  grDevices utils    datasets  methods

[8] base    

other attached packages:
[1] annotate_1.18.0    xtable_1.5-2        hgu95av2.db_2.2.0  
[4] AnnotationDbi_1.2.1 RSQLite_0.6-8      DBI_0.2-4          
[7] Biobase_2.0.1      

loaded via a namespace (and not attached):
[1] splines_2.7.0

------------------------------------------------------------------------
---------------

Best Regards,
Chanchal 
===============================
Chanchal Kumar, Ph.D. Candidate
Dept. of Proteomics and Signal Transduction
Max Planck Institute of Biochemistry
Am Klopferspitz 18
82152 D-Martinsried (near Munich)
Germany
e-mail: chanchal@biochem.mpg.de
Phone: (Office) +49 (0) 89 8578 2296
Fax:(Office) +49 (0) 89 8578 2219
http://www.biochem.mpg.de/mann/
===============================

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Anna Freni Sterrantino
Ph.D Student 
Department of Statistics
University of Bologna, Italy
via Belle Arti 41, 40124 BO.

 





  

 

 

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