Wednesday, October 3, 2012

Problem with loading data into CummeRbund in R

If you have performed RNA-Seq pipeline using Topahat/Bowtie, Cufflinks, Cuffmerge, Cuffdiff and you are trying to load your data into CummeRbund package for R for visualization, you may get the following output:

> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
 

> cuff_data <- readCufflinks('diff_out')
Creating database diff_out/cuffData.db
Error in sqliteNewConnection(drv, ...) :
  RS-DBI driver: (could not connect to dbname:
unable to open database file
)


The problem may seem difficult to solve but actually you haven't set the correct working directory.
Do:
getwd()
to get the working directory,
and the setwd() 
to set the working directory.

You have to set the working directory where your diff_out folder is! But not the diff_out folder itself!

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