Hi Bogdan - you answered by yourself: you don't have replicates, so how can 
any software estimate any kind of (common or tagwise) dispersion ? there is 
one section on edgeR manual with interesting hints about what you can - and 
can not - evaluate with such 'minimal' experiments

My two cents, regards,

Alessandro
-----------------------------------------------------
Alessandro Guffanti - Bioinformatics, Genomnia srl
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http://www.genomnia.com
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-----Original Message-----
 From: Bogdan Tanasa <tanasa@gmail.com>
 To: <bioconductor@stat.math.ethz.ch>
 Date: Fri, 6 Jul 2012 15:57:13 -0700
 Subject: [BioC] Fwd: edgeR dispersions


Dear all,

 I would appreciate a suggestion about edgeR : I have a GRO-seq dataset (CTL
 vs TREAT, no replicates, just 1 sample for CTL and 1 sample for TREAT
 condition),
 and I am assessing the differential expression by using edgeR, but I am
 getting an error : any suggestion would be appreciated. thanks very much !

 > d <- estimateCommonDisp(d)
 Warning message:
 In estimateCommonDisp(d) :
   There is no replication, setting dispersion to NA.

 > de.com <- exactTest(d)
 Error in if (any(dispersion < 0)) stop("dispersion must be non-negative") :
   missing value where TRUE/FALSE needed

 > de.com <- exactTest(d,dispersion=0)
 Error in binomTest(s1[pois], s2[pois], p = n1/(n1 + n2)) :
   y1 and y2 must be non-negative

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