I think it looks like a "rouge" tag, since it is not found in all the replicates (biological or technical?). Is the gene (or tag) annotated? Depending on the cutting enzyme, is it the most 3' canonical, or could it be caused by incomplete digestion?
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Laurent Gautier Sent: 21. februar 2011 15:36 To: [email protected] Subject: [Bioc-sig-seq] RNASeq, differential expression between group, and large variance within groups Dear List, We are looking at tag-based RNASeq data, and after running popular packages for finding differential expression (edgeR, and DEGseq) we were looking that the actual counts for the significant ones. We are observing a somewhat extreme variance within each group for those (say one sample with high count for gene X while others have zero count). For example, gene X flagged as differentially expressed has the following counts (adjusted p-value with DGESeq is 9.401479e-10): 0 grp_A 0 grp_A 0 grp_A 92207 grp_B 0 grp_B 0 grp_B The underlying binomial is obviously not like the almost-Gaussian assumed in microarrays/t-test-like approaches, but this kind of outcome is somehow intriguing me. Do people here have experience to share regarding how well such gene hold through the qPCR verification step ? Laurent PS: In case the sessionInfo() matters R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_DK.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_DK.UTF-8 LC_COLLATE=en_DK.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_DK.UTF-8 [7] LC_PAPER=en_DK.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_DK.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq_1.2.1 locfit_1.5-6 lattice_0.19-17 akima_0.5-4 [5] Biobase_2.10.0 loaded via a namespace (and not attached): [1] annotate_1.28.0 AnnotationDbi_1.12.0 DBI_0.2-5 [4] genefilter_1.32.0 geneplotter_1.28.0 grid_2.12.1 [7] RColorBrewer_1.0-2 RSQLite_0.9-4 splines_2.12.1 [10] survival_2.36-2 tools_2.12.1 xtable_1.5-6 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
