I have collected over 1000 samples for my analysis, each dataset contain around 200 samples. When i did arrayQualityMetrics, my system got hanged. And my system is 6GB RAM, can anyone please tell me how much maximum RAM is needed to run for this particular analysis??
The package is designed with datasets of a few dozen arrays in mind. This concerns not only memory consumption but also the choice & layout of the diagnostic plots it produces. For a large project like yours, you'll need to adapt it for your data. I recommend:
Run the arrayQualityMetrics function on a subset of, say, 24 arrays, to see that it works for you in principle. Measure the amount of memory it uses. Familiarize yourself with the plots.
Read the vignette "Advanced topics: Customizing arrayQualityMetrics reports...", identify the plots you need, and produce them directly - this should be quicker and less memory intensive
You could also repeat step 1. for 48, 96, 192,... arrays, plot the relationship and extrapolate the amount of memory you need.
Thank you so much.. :-)