[BioC] gage package: biological replicates and technical replicates

Luo Weijun luo_weijun at yahoo.com
Sat Dec 4 06:15:12 CET 2010

Hi Heyi,
We considered this scenario with argument 'weights' in the gage function. To use this argument, we need to manually pair arguments 'ref' and 'samp', and set compare='paired'. Check the help information for the function by typing '?gage' within R. take a simple example, we have 7 samples/columns C1a, C1b, C2a, C2b, T1a, T1b, T2a (T2b is missing somehow). C means control, T means treated, 1 and 2 are biological replicates, a and b are technical replicates. When C and T samples are matched, i.e. C1-T1, C2-T2, we set: ref=c(1,1,2,2,3,4), samp=c(5,6,5,6,7,7), weights=c(0.5,0.5,0.5,0.5,1,1), compare='paired'. When C and T samples are unmatched, ref=rep(1:4, each=3), samp=rep(5:7, 4), weights=rep(c(0.5, 0.5, 1), 4), compare='paired'.
There is no need to set weights option if T2b exists, as every C and T sample has the same weight. Hope this helps.

--- On Fri, 12/3/10, heyi xiao <xiaoheyiyh at yahoo.com> wrote:

> From: heyi xiao <xiaoheyiyh at yahoo.com>
> Subject: gage package: biological replicates and technical replicates
> To: bioconductor at stat.math.ethz.ch
> Date: Friday, December 3, 2010, 4:44 PM
> I am doing gene set analysis using
> gage package. I have two sample groups, controls and treated
> samples. I have one question about using the default 1-on-1
> (pairwise) comparison for unpaired samples. My samples have
> both biological replicates and technical replicates. Shall I
> treat them the same way? Woud that be a little improper?
> Heyi

More information about the Bioconductor mailing list