[BioC] Biological replicates with Gage

[Luo Weijun]

Hi Leutz,
Thanks for your interest in GAGE. For your question, GAGE decomposes group-vs-group comparison into sample-vs-sample (pair-wise) comparison. You need to specify control and treated sample column indices using 'ref' and 'samp' arguments. 
The following code chunk show you some example run on your data. Check the help information of 'gage' function and the package vignette for more details. HTH.
Weijun

library(gage)
library(gageData)
data(kegg.gs)

#1 time point
cn=colnames(yourArrayData)
c1=grep(' c1',cn, ignore.case =T)
t1=grep('t1',cn, ignore.case =T)
gse16873.kegg.p = gage(yourArrayData, gsets = kegg.gs, ref = c1, samp = t1)
#you need to specify argument compare = "unpaired" if your c1 and t1 samples are not paired (1-on-1 matched) by design.

#multiple time points altogether
refList=list(c1, c8, c16, c24)
sampList=list(t1, t8, t16, t24)
sampnames=pc("t1vsc1","t8vsc8","t16vsc16","t24vsc24")
gagePipe(yourArrayData, gsname = "kegg.gs", dataname = "yourStudy", 
    sampnames = sampnames, ref.list = refList, samp.list = sampList)
#again, you need to specify argument compare = "unpaired" if your control and treated samples are not paired.


--- On Sun, 7/24/11, Leutz Buon <lb089 at research.dfci.harvard.edu> wrote:

> From: Leutz Buon <lb089 at research.dfci.harvard.edu>
> Subject: Biological replicates with Gage
> To: "Weijun Luo" <luo_weijun at yahoo.com>
> Date: Sunday, July 24, 2011, 8:01 PM
> 
> Hi,
> I'm doing a gene set analysis with GAGE. With Control and
> treated samples at different time points :
> 1hr,8hr,16hr,24hr.
> For example:
> c1r1 (control replicate 1 at 1hr)
> ...............................
> c1r3 (control replicate 3 at 1hr)
> 
> t1r1 (treated replicate 1 at 1hr)
> ...............................
> t1r3 (treated replicate 3 at 1hr)
> 
> And so on for time 8,16, and 24hr
> Does GAGE automatically pool replicates and
> do(matched)compare? If not, please advise.
> Thanks,
> -LB.
> 
> 
> The information in this e-mail is intended only for th...{{dropped:14}}