[BioC] cummeRbund Error in Volcano Plot

[Loyal Goff]

Hi,
(Thank you for forwarding this to me Valerie, I did in fact miss.)

You must provide two additional arguments to csVolcano.  You need to specify which two sample for which you would like to plot the log fold change, since this is a pairwise comparison plot.

Please try something like the following:

cuff<-readCufflinks()
gene <- genes(cuff)
v<-csVolcano(gene, "sampleA", "sampleB")
v


I hope this helps.

Cheers,
Loyal


On Dec 2, 2011, at 11:46 AM, Valerie Obenchain wrote:

> 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
>> 
>