These events indicate that a file "Li_sum.txt" is not available in your current working folder. Inspection of the goseq.Rnw shows that the Rnw file does not specify any R computations to be performed when processed by Sweave; it is a "woven" version of some other program. Therefore the Rnw file can be transformed to pdf despite the absence of the file to be read. At present it just shows how you could conduct an analysis if you had files analogous to the ones described in the workflow. Contact the goseq developers directly for further concerns.
On Fri, Mar 5, 2010 at 10:17 PM, joseph <[email protected]> wrote: > Trying to duplicate the example in the goseq vignette: > >> table.summary = read.table("Li_sum.txt", sep = "\t", stringsAsFactors = >> FALSE, header = TRUE) > Error in file(file, "rt") : cannot open the connection > In addition: Warning message: > In file(file, "rt") : > cannot open file 'Li_sum.txt': No such file or directory >> sessionInfo() > R version 2.10.1 Patched (2010-01-25 r51042) > x86_64-apple-darwin9.8.0 > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] mgcv_1.6-1 edgeR_1.4.7 goseq_0.1.5 BiasedUrn_1.03 > loaded via a namespace (and not attached): > [1] grid_2.10.1 lattice_0.18-3 limma_3.2.1 > Matrix_0.999375-33 nlme_3.1-96 tools_2.10.1 >> > > Thanks for your help > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
