[BioC] variation between cells compared to samples

[Wolfgang Huber]

Hi Pete

1. how do the two SCV curves look like if you plot them into one panel?
2. as Steve suggests, you could compute the 4x4 distance matrix between all pairs of experiments, and perhaps visualise the distances with multidimensional scaling or dendrogram / hierarchical clustering. For this, I'd use the variance stabilising transformation as described in Section 7 ("Sample Clustering") of the vignette, or the man page of the "getVarianceStabilizedData function".

             Best wishes
               Wolfgang

Il giorno Feb 19, 2010, alle ore 7:23 PM, Pete Shepard ha scritto:

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?

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Wolfgang Huber
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