[BioC] DESeq2

[Martin Morgan]

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 at 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.
>>
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