[BioC] variation between cells compared to samples

[Steve Lianoglou]

Hi,

On Fri, Feb 19, 2010 at 1:23 PM, Pete Shepard <peter.shepard at gmail.com> wrote:
> Hi All,
>
> I am comparing four RNAseq experiments, exp # 1 and 2 are done using
> protocol A and experiment 3 and 4 are done using protocol B. Experiments 1
> and 3 are done using stem cells and experiment 2 and 4 are done using neural
> cells. I would like to see if there is more variation between the two types
> of protocols compared to the two types of cells. I have used the DESEQ
> package to plot the squared coefficient of variation against the base mean
> but I am wondering if there is a single metric I can use to compare the
> variations?

Here's a simple/gross test: what if you calculate the gene expression
(let's say rpkm) of the genes in each dataset then cluster the
samples.

Do the samples cluster/pair-off by cell line, or by protocol?

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact