Hi am new to R and using cummeRbund to visualize my data from the cuffdiff output to check the DE lot of genes. The problem is I have a huge sample lot where I have 27 different conditions so when I used read readCufflinks to create the cuffdata.db it takes a long time and creates a database with all the files of around 14 GB. Now the problem is earlier each time R was crashing as the database build up was consuming lot of memory and it was a huge one. Now that it was build up while working with R for all the visualization codes suddenly it ran out of memory and stopped so had to quit R. Now that my cuffdata.db is already created how to work with it in the new session of R since while it shut down I could not save the workspace and again rebuilding the database will not be a good idea. So can you tell me any idea about how to work with the database , any command to do so without creating it again and not putting a stress on the memory. And so that I can directly write the commands to visualize the data. My database variable is cuff_data. Since now each time I m trying to to rebuild it , it getting segfault.
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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
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