[BioC] edgeR and FDR values always equals 1

[A Gossner]

Gordon K Smyth <smyth at ...> writes:

> 
> Hi Anton,
> 
> This is the way the software is designed to behave when there is no 
> differential expression between your groups.  The software is telling you 
> that there is no statistically significant differential expression.
> 
> The reason for this result seems to be the enormously high values for the 
> dispersions.  The values you have (3.5 up to 7) are an order of magnitude 
> higher than my lab has ever seen for RNA-seq or SAGE-seq data.  This 
> represents enormous inconsistency between your replicate samples, and 
> suggests something might wrong with your data setup.  Another curious fact 
> is that all the putative differential expression is one direction, down in 
> the INF group.
> 
> To examine your data setup, you might try an MDS plot (plotMDS).  This 
> would show you if you have one or more outlier libraries, or if one or 
> more libraries are mis-classified into groups.  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.
> 
> To combat the fact that much of the differential expression is in one 
> direction, you might try normalizing, calcNormFactors().
> 
> Best wishes
> Gordon
> 
> > Message: 25
> > Date: Thu, 11 Nov 2010 10:44:07 +0000
> > From: A Gossner <a.gossner at ...>
> > To: bioconductor at ...
> > Subject: [BioC] edgeR and FDR values always equals 1
> >
> > Hi,
> >
> > While using edgeR to analysis my Tag-seq data, no matter which way I
> > analyse the data common or tagwise dispersion the FDR value is always 1.
> > Typical output is shown below;
> >

> 
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