Thanks. ________________________________ From: Martin Morgan <mtmorgan@fhcrc.org> To: Michael Love <michaelisaiahlove@gmail.com> uctor@r-project.org" <bioconductor@r-project.org> Sent: Monday, April 15, 2013 11:21 AM Subject: Re: [BioC] DESeq2 On 04/15/2013 08:16 AM, Michael Love wrote: > hi Yemmy, > > There was a missing 'as.data.frame' in the vignette which I corrected in > version 1.0.4. The 'res' object is a DataFrame which can be exported after > conversion to a data.frame. > > so you should do: > > write.csv(as.data.frame(res), file="AN_WFDEgenes.csv") > > Also, since version 1.0.3, we decided to rename the package class to > 'DESeqDataSet' to save keystrokes and compress some long function names.  A > global find/replace of 'DESeqSummarizedExperiment' should take care of any > problems. > > Mike > > > > On Mon, Apr 15, 2013 at 4:16 PM, Yemmy [guest] <guest@bioconductor.org>wrote: > >> >> Hi All, >> >> I decided to give DESeq2 a shot but my progress has been limited due to >> this annoying error whenever I want to save my results. Please have a look. >> >> write.csv(res, file="AN_WFDEgenes.csv") >> Error in as.data.frame.default(x[[i]], optional = TRUE) : >>    cannot coerce class 'structure("DataFrame", package = "IRanges")' into a >> data.frame >> >> I don't know how to go about it. >> >>  -- output of sessionInfo(): >> >>> sessionInfo() >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-w64-mingw32/x64 (64-bit) DESeq2 is not available via biocLite until R-3.0.0. You should install R-3.0.0 and use   source("http://bioconductor.org/biocLite.R")   biocLite("DESeq2") to install Bioconductor (and other) packages. Using other approaches will eventually lead to tears, even if this is not the cause of your current problems. Martin >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats    graphics  grDevices utils    datasets  methods base >> >> other attached packages: >>  [1] DESeq2_1.0.2            RcppArmadillo_0.3.800.1 Rcpp_0.10.3 >>  [4] GenomicRanges_1.10.7    IRanges_1.16.6 pasilla_0.2.15 >>  [7] DESeq_1.10.1            lattice_0.20-10        locfit_1.5-9 >> [10] DEXSeq_1.4.0            Biobase_2.18.0 BiocGenerics_0.4.0 >> >> loaded via a namespace (and not attached): >>  [1] annotate_1.36.0      AnnotationDbi_1.20.7 biomaRt_2.14.0 >>  [4] DBI_0.2-5            genefilter_1.40.0    geneplotter_1.36.0 >>  [7] grid_2.15.2          hwriter_1.3          parallel_2.15.2 >> [10] RColorBrewer_1.0-5  RCurl_1.95-4.1      RSQLite_0.11.2 >> [13] splines_2.15.2      statmod_1.4.17      stats4_2.15.2 >> [16] stringr_0.6.2        survival_2.36-14    tools_2.15.2 >> [19] XML_3.96-1.1        xtable_1.7-1 >>> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >     [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 [[alternative HTML version deleted]]