[Bioc-sig-seq] goseq or edgeR error

[Vincent Carey]

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 <jdsandjd at yahoo.com> 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
>
>
>
>
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