Hi,

Thank you for response.
Its working.
I thought that it should work without passing the sample names.

Regards,

Chintan Vora
Sr. Research Associate
Xcelris Labs Ltd.
Old Premchandnagar Road,
Bodakdev, Ahmedabad-380 054 India.
Tel: +91-79-66197777/66311114
Fax: +91-79-66309341
Email: chintan.vora@xcelrislabs.com
Website: www.xcelrisgenomics.com


On 12/02/2011 11:41 PM, Loyal Goff wrote:
> 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
>>>
>
>


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