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 [[alternative HTML version deleted]]