Dear Igoff, I have a trouble to understand some value in cummeRbund - I am sorry for disturbing, but I did not find any answer on Internet. I have two mouses paired-end sequenced. I mapped with Tophat2 - make Cufflinks - and Cufdiff (one replicates - two conditions) - and CummeRbund. It is very nice graphs and outputs, but I would like to get just one number, which tell me total transcript expression for mouse1 and for mouse2 and compare it. It is possible to take output form Cufflinks - transcripts.gtf and extract FPKM value for all genes and do sum of all FPKM's? Something like - awk 'OFS="t"{sum+=$16}END {print sum}' transcripts.gtf. And also when I print in R command replicates(cuff) - what does it mean value total_mass, norm_mass and internal_scale? Can I use value total_mass to explain differences between transcripts? Are those values somewhere detailed explained? Thank you so much for any help - I am little desperate :-( Kind Regards, Petr. -- output of sessionInfo(): > session(info) Error: could not find function "session" > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] cummeRbund_2.5.3 Gviz_1.7.10 rtracklayer_1.23.22 [4] GenomicRanges_1.15.44 GenomeInfoDb_0.99.30 IRanges_1.21.44 [7] fastcluster_1.1.13 reshape2_1.2.2 ggplot2_0.9.3.1 [10] RSQLite_0.11.4 DBI_0.2-7 BiocGenerics_0.9.3 loaded via a namespace (and not attached): [1] AnnotationDbi_1.25.17 BatchJobs_1.2 [3] BBmisc_1.5 Biobase_2.23.6 [5] BiocParallel_0.5.20 biomaRt_2.19.3 [7] Biostrings_2.31.22 biovizBase_1.11.15 [9] bitops_1.0-6 brew_1.0-6 [11] BSgenome_1.31.13 cluster_1.15.2 [13] codetools_0.2-8 colorspace_1.2-4 [15] dichromat_2.0-0 digest_0.6.4 [17] fail_1.2 foreach_1.4.1 [19] Formula_1.1-1 GenomicAlignments_0.99.38 [21] GenomicFeatures_1.15.15 gtable_0.1.2 [23] Hmisc_3.14-3 iterators_1.0.6 [25] labeling_0.2 lattice_0.20-29 [27] latticeExtra_0.6-26 MASS_7.3-31 [29] matrixStats_0.8.14 munsell_0.4.2 [31] plyr_1.8.1 proto_0.3-10 [33] RColorBrewer_1.0-5 Rcpp_0.11.1 [35] RCurl_1.95-4.1 R.methodsS3_1.6.1 [37] Rsamtools_1.15.41 scales_0.2.3 [39] sendmailR_1.1-2 splines_3.1.0 [41] stats4_3.1.0 stringr_0.6.2 [43] survival_2.37-7 tools_3.1.0 [45] VariantAnnotation_1.9.49 XML_3.98-1.1 [47] XVector_0.3.7 zlibbioc_1.9.0 > -- Sent via the guest posting facility at bioconductor.org.