[BioC] cummeRbund errors

[Loyal Goff]

Hi Li,
Sorry for the delayed response.  I have not been able to reproduce the first error, can you email me directly your cuffData.db file and I will see if I can figure out what's going on..

As for the second error.  This arises from the fact that the csDensity function is dying in the middle of a transaction.  Another call to readCufflinks() should re-establish a connection to the database and resolve this issue.


Cheers,
Loyal

On Jun 5, 2012, at 7:40 PM, Wang, Li wrote:

> Dear list members
> 
> I am struggling with cummeRbund. I tried some codes listed here, and am confronted with some errors. 
> 
>> cuff_data <- readCufflinks('diff_out')
>> csDensity(genes(cuff_data))
> 
> Error in dat$fpkm + pseudocount : non-numeric argument to binary operator
> 
>> diffGeneIDs <- getSig(cuff_data, level="genes", alpha=0.05)
>> diffGenes <- getGenes(cuff_data, diffGeneIDs)
> 
> Error in sqliteExecStatement(conn, statement, ...) : 
> RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)
> 
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] cummeRbund_1.2.0 reshape2_1.2.1   ggplot2_0.9.1    RSQLite_0.11.1   DBI_0.2-5       
> 
> loaded via a namespace (and not attached):
> [1] colorspace_1.1-1   dichromat_1.2-4    digest_0.5.2       grid_2.15.0       
> [5] labeling_0.1       MASS_7.3-18        memoise_0.1        munsell_0.3       
> [9] plyr_1.7.1         proto_0.3-9.2      RColorBrewer_1.0-5 scales_0.2.1      
> [13] stringr_0.6 
> 
> I cannot figure out the reason, could anyone give me some hints?
> 
> Thanks in advance!
> 
> Best wishes
> Li
> 
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