Question

arrayQualityMetrics package in bioconductor for whole genome trancriptomics?

1

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8.0 years ago

hakimelakhrass ▴ 80

So I have an experiment with 9 replicates and 5 time points. It is whole genome and I can't find any package to do quality control. The above package works on my array type (hugene 2.0) but it won't work for my amount of data, I keep getting memory full errors. Any help would be great!

Thanks

R microarry affy • 1.3k views

ADD COMMENT • link updated 7.9 years ago by Adamc ▴ 680 • written 8.0 years ago by hakimelakhrass ▴ 80

score 1 · Answer 1 · 2016-05-19

Do you know at which point you're having memory issues? You can always subset them and run them in multiple groups- that will work for getting a sense of the un-normalized data at least. For a normalization method like RMA which works across all of the samples, you'll need to be able to read in all the files. Also try closing everything you have running the background, and make sure you're running a 64-bit version of R. If you still have issues, you might need to track down a computer with 6 or 8GB RAM.