Thanks Wolfgang,

The distance matrix works nicely however, I am having trouble plotting the
two scv curves to one panel, any suggestions. I can give to cds "cds <-
newCountDataSet( countsTable, conds )" a set of count data based on one set
of conditions conds <- c("Old", "Old", "New", "New" )
obtain the variance " cds <- estimateVarianceFunctions( cds )" and plot them
scvPlot(cds)

I can then change the conds <- c("Stem", "Stem", "Neuron", "Neuron" ) and
repeat for this the same steps as above. But, I am having trouble plotting
the two sets of variances against eachother, on the same graph?

P

On Fri, Feb 19, 2010 at 2:35 PM, Wolfgang Huber <whuber@embl.de> wrote:

> 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?
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> Wolfgang Huber
> whuber@embl.de
>
>
>
>

	[[alternative HTML version deleted]]

