[BioC] edgeR and FDR values always equals 1

[Mark Robinson]

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?

Cheers,
Mark

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
e: mrobinson at wehi.edu.au
e: m.robinson at garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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