Dear All

I have a Dataset with 3 conditions (2,3 and 4 replicates). I'm mainly interested in the
exon expressions of one particular gene.
Looking at the DEXSeqResult table I noticed that NO log2FCs for all exons of my gene
of interest where estimated. However, I do get a pvalue/adjpvalue for most of the exons.
(see example below).

So my questions are:
- Is this a serious problem?
- Why do I not get log2FCs for these exons?
- How do I fix this?

The gene contains 65 exons and while some exons have 0 read counts others have from
counts from 5 up to 120.

#==================================================================
3 EXAMPLE exons from DEXSeqResult:


        exonBaseMean    dispersion      stat    pvalue  padj    QQ      Qq      qq      log2fold_Qq_QQ  log2fold_qq_QQ  countData.002_EX        countData.004_EX        countData.005_EX        countData.043_EX        countData.044_EX        countData.103_EX        countData.248_EX        countData.386_EX
XLOC_105064:E001        85      0.003103958     3.3720003871    0.1852590444    0.9633381947    NA      NA      NA      NA      NA      83      90      85      86      64      76      68      128
XLOC_105064:E002        45.25   0.0011722726    0.1316948642    0.9362736987    0.999516858     NA      NA      NA      NA      NA      33      40      39      54      33      49      39      75
XLOC_105064:E003        47.75   0.0105234376    0.68404406      0.7103325559    0.999516858     NA      NA      NA      NA      NA      41      49      31      60      35      68      30      68


#==================================================================
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] C

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

other attached packages:
 [1] DEXSeq_1.10.6             BiocParallel_0.6.1
 [3] DESeq2_1.4.5              RcppArmadillo_0.4.300.8.0
 [5] Rcpp_0.11.2               GenomicRanges_1.16.3
 [7] GenomeInfoDb_1.0.2        IRanges_1.22.9
 [9] Biobase_2.24.0            BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.26.0 BBmisc_1.7           BatchJobs_1.2
 [4] Biostrings_2.32.0    DBI_0.2-7            RColorBrewer_1.0-5
 [7] RCurl_1.95-4.1       RSQLite_0.11.4       Rsamtools_1.16.1
[10] XML_3.98-1.1         XVector_0.4.0        annotate_1.42.0
[13] biomaRt_2.20.0       bitops_1.0-6         brew_1.0-6
[16] checkmate_1.0        codetools_0.2-8      compiler_3.1.0
[19] digest_0.6.4         fail_1.2             foreach_1.4.2
[22] genefilter_1.46.1    geneplotter_1.42.0   grid_3.1.0
[25] hwriter_1.3          iterators_1.0.7      lattice_0.20-29
[28] locfit_1.5-9.1       plyr_1.8.1           sendmailR_1.1-2
[31] splines_3.1.0        statmod_1.4.20       stats4_3.1.0
[34] stringr_0.6.2        survival_2.37-7      tools_3.1.0
[37] xtable_1.7-3         zlibbioc_1.10.0
#==================================================================

Many thanks,

Fabian



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