[BioC] edgeR: plotBCV, gof() and plotMDS, for outlier detection

[Yunshun Chen]

Hi Sindre,

It seems that you have one suspicious sample in your data according to your
MDS plot. 
That sample (on the very right of the MDS plot) is very likely to be an
outlier, hence vastly increases your dispersion estimates.

For statistical analysis purpose, it would be better to take that sample
out.

Regards,
Yunshun Chen


Message: 4
Date: Sun, 02 Mar 2014 21:00:50 +0100
From: Sindre Lee <sindre.lee at studmed.uio.no>
To: <bioconductor at r-project.org>
Subject: [BioC] edgeR: plotBCV, gof() and plotMDS, for outlier
	detection
Message-ID: <b618869c628acccf65b86037c4774909 at ulrik.uio.no>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Hello!
I have been struggling with one of the skeletal muscle biopsies in my study.
The RNA quality is very good and looking at tissue specific gene expression
they are all there, although some with very different values for some genes
compared the other biopsies.

Please see the attached plots using edgeR. The gof() calculation gave 0
"TRUE" in the $outlier table.


Can anyone shed some light on this? Thank you very much.
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