[BioC] problems getting new intact networks from ppiData

Sara JC Gosline sara.gosline at mail.mcgill.ca
Wed Dec 2 21:47:34 CET 2009


Hello,

I'm trying to use the ppiData package and am having trouble getting 
newer datasets from intact. 

 >library(ppiData)
 >collectIntactPPIData("EBI-2007879")
Error in b2pList[[i]][[j]] : subscript out of bounds

My sessionInfo() is at the end of this email.

It appears that this later dataset is not in the downloaded repository. 
The man pages refer to this tableList.rda which is generated by 
parseIntAct.R.  I found parsingIntAct.R but the output doesn't appear to 
match tableList.rda. 

Is there a simple way to use this package to access datasets that are 
not in tableList.rda?

thanks,
sara


 > sessionInfo()
R version 2.7.0 (2008-04-22)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;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] ppiData_0.1.13   Rgraphviz_1.18.0 graph_1.18.1

loaded via a namespace (and not attached):
[1] cluster_1.11.10 tools_2.7.0



More information about the Bioconductor mailing list