Entering edit mode
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)
datakegg.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}}