I am in the process of performing QC for > 1500 samples of HTA 2.0 array data. I am using oligo package and additional packages like arrayQualitymetrics to perform QC. I also using a linux system, and since most of these packages run single threaded - it takes a very a long time for all the process to complete.

Since arrayQualitymetrics produces a very good report, I am using it and it has been over a day since the analysis has started to run. can that tool handle such a large data set ? Can you please provide me with some good practices for big sample size microarray analysis ?

Thanks!

Have a look at the vignette Advanced topics: Customizing arrayQualityMetrics reports and programmatic processing of the output of the package. You could eliminate certain parts of the report that take a very a long time, or write code to parallelize them.