[BioC] edgeR and FDR values always equals 1

[A Gossner]

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;

>  d$prior.n
[1] 10
>  head(d$tagwise.dispersion)
[1] 4.360269 5.192625 5.006097 5.006097 3.960243 5.192625
>  summary(d$tagwise.dispersion)
    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
   3.511   4.665   5.006   4.926   5.193   7.240
>  d$common.dispersion
[1] 4.884378
>  prior.n <- estimateSmoothing(d) prior.n
[1] 3.575805e-05
>
>  de.tagwise <- exactTest(d, common.disp = FALSE)
Comparison of groups:  INF - CON
>  topTags(de.tagwise)
Comparison of groups:  INF - CON
                         logConc      logFC       PValue FDR
CATGGGAACAATAAACTCCAC -17.88755 -10.968487 0.0004244306   1
CATGTCTGCCCAAGCACCTAC -32.20325 -35.625605 0.0009657247   1
CATGTTCCTGGTAGCACAAAT -18.89883  -9.075728 0.0011952265   1
ATTGATGTTCTACACCACATG -32.92827 -34.175568 0.0014322637   1
AAAAGGATGACTTCACTCATG -32.99637 -34.039364 0.0016256396   1
CATGATGTGACTTTTAAGTCC -32.81141 -34.409298 0.0018494476   1
AAACCCAGGGAAAGAAGCATG -32.98827 -34.055559 0.0018645461   1
CTTTTTAGATCAAAAAGCATG -33.17368 -33.684744 0.0022498203   1
CGGTCTTATTTAGGAGACATG -32.83447 -34.363162 0.0026414159   1
CATGCTCTTTATCACACCCCC -33.05201 -33.928086 0.0027765733   1
>  sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-mingw32

locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] edgeR_1.6.15

loaded via a namespace (and not attached):
[1] limma_3.4.5

Would be grateful for any suggestions?

Regards

Anton




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