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)
>
> 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.
>
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