Hello all, I am having problem with the DEXseq program using TRT functions, and I was hoping that somebody could help me once more. :) I successfully ran through a full analysis of one time point of my dataset, and was hoping ideally to extend the analysis to my full time course, using the GLM test. As mentioned in earlier discussion, I have sourced the TRT functions from the svn repository, and successfully completed the estimateDispersionsTRT. However, I ran into this error when running fitDispersionFunction: Am I doing something wrong? Thanks for the help Uma > ecs.p = fitDispersikonFunction(ecs.p) Error: could not find function "fitDispersikonFunction" > ecs.p = fitDispersionFunction(ecs.p) Error in glmgam.fit(mm, disps[good], start = coefs) : unused argument (start = coefs) Error in fitDispersionFunction(ecs.p) : Failed to fit the dispersion function > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] DEXSeq_1.8.0 Biobase_2.22.0 BiocGenerics_0.8.0 statmod_1.4.18 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationDbi_1.24.0 biomaRt_2.18.0 [4] Biostrings_2.30.1 bitops_1.0-6 DBI_0.2-7 [7] DESeq_1.14.0 DESeq2_1.2.5 genefilter_1.44.0 [10] geneplotter_1.40.0 GenomicRanges_1.14.3 grid_3.0.2 [13] hwriter_1.3 IRanges_1.20.6 lattice_0.20-24 [16] locfit_1.5-9.1 RColorBrewer_1.0-5 Rcpp_0.10.6 [19] RcppArmadillo_0.3.920.3 RCurl_1.95-4.1 Rsamtools_1.14.2 [22] RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 [25] stringr_0.6.2 survival_2.37-4 XML_3.98-1.1 [28] xtable_1.7-1 XVector_0.2.0 zlibbioc_1.8.0 [[alternative HTML version deleted]]

Hi Uma On 26/12/13 21:18, Uma Shankavaram wrote: > I am having problem with the DEXseq program using TRT functions, and I was > hoping > that somebody could help me once more. :) I successfully ran through a > full analysis of one time point of my dataset, and was hoping ideally to > extend the analysis to my full time course, using the GLM test. > As mentioned in earlier discussion, I have sourced the TRT functions from > the svn repository, and successfully completed the > estimateDispersionsTRT. However, I ran into this error when running > fitDispersionFunction: [...] What exactly do you mean by "sourced the TRT functions from the svn repository"? Please simply use the standard release version of DEXSeq, 1.8.0, which now uses as default method what used to be called "TRT" at some point during development. (See Appendix C of the vignette for details.) If the problem persists, please ask again. Simon