[BioC] cummeRbund Error in Volcano Plot

[Valerie Obenchain]

Hi,

I'm cc'ing Loyal (package maintainer) in case he didn't see this message.

Valerie


On 11/30/2011 11:03 PM, Chintan Vora - Xcelris wrote:
> Hi,
>
> I am trying to plot different graphs using cummerRbund for bacterial
> transcriptome.
> I get all the plots except the volcano plot.
>
> I am using : tophat-1.3.3.Linux_x86_64, samtools-0.1.12a,
> cufflinks-1.2.0.Linux_x86_64
>
> I get following error:
>
> library("cummeRbund")
> cuff = readCufflinks()
> cuff
> gene = genes(cuff)
> v = csVolcano(gene)
> v
> Error in grid.pretty(range) :
>     infinite axis extents [GEPretty(-1.79769e+308,1.79769e+308,5)]
>
> Can someone please explain where am i going wrong?
>
> R session info is given below:
>
> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>    [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>    [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>    [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>    [7] LC_PAPER=C                 LC_NAME=C
>    [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] cummeRbund_1.0.0 ggplot2_0.8.9    proto_0.3-9.2    reshape_0.8.4
> [5] plyr_1.6         RSQLite_0.10.0   DBI_0.2-5
>