[BioC] No significant p-values

Steve Lianoglou lianoglou.steve at gene.com
Fri Jun 27 18:24:41 CEST 2014


On Fri, Jun 27, 2014 at 7:06 AM, Lucia Peixoto <luciap at iscb.org> wrote:
> Hi Dave,
> If in your PCA your samples do not cluster by treatment, you likely have
> some sort of unwanted variation or batch effect masking the effect of the
> treatment in your data. I am not sure more samples will help.
> Have you taken a look at the PC loadings past 1 and 2 to see if there is
> any PC that captures your treatment? do you have any positive controls? are
> you sure your treatment actually causes measurable differences in gene
> expression?
> The only think I believe will help is RUVSeq:
> http://www.bioconductor.org/packages/devel/bioc/html/RUVSeq.html

Not the only thing ... this is slightly different, but also something
to keep an eye on "in this context" (ie. removing nuisance effects):

svaseq: removing batch effects and other unwanted noise from sequencing data

Thank you for bringing my attention to RUVSeq, though, as I haven't
seen it before.


Steve Lianoglou
Computational Biologist

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