[BioC] edgeR and FDR values always equals 1

Mark Robinson mrobinson at wehi.EDU.AU
Sun Nov 14 12:07:14 CET 2010

Hi Anton.

I've had a quick look at both batches of your plots.  The replicates are quite variable, but something is indeed unusual.  Can you post your full set of commands used?


On 2010-11-13, at 9:51 PM, A Gossner wrote:

> Hi Gordon,
> Gordon K Smyth <smyth at ...> writes:
>> Another curious fact is that all the putative differential expression is one  
>> direction, down in the INF group.
> Have plotted the fold change smear plots and the top 500 DE tags seem to lie in
> a very strange line. Not sure what the cause/effect this is due to?
>> To examine your data setup, you might try an MDS plot (plotMDS).  
> Have plotted the MDS plots and there are obviously differences between the
> control samples (highlighted) and the infected samples but also large
> differences within the groups especially in dimension 1, especially if judged by
> the scale in the edgeR manual pdf.
> You might also explore 
>> your data using smear plots plotSmear() to get a better idea of what is 
>> happening.  You must have some very unusual samples.
> All plots are in a pdf saved on the following FTP server.
> ftp.ed.ac.uk
> Login using the username 'anonymous' and use your email address as password.
> get /edupload/edgerplots.pdf
>> To combat the fact that much of the differential expression is in one 
>> direction, you might try normalizing, calcNormFactors().
> will try normalizing as you suggest.
> Thanks for you help.
> Anton
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Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
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