Question: Quantiles Normalization On Massive Dataset
2
gravatar for Paul
7.7 years ago by
Paul750
United States
Paul750 wrote:

Hi,

I've got a massive dataset of 160 Affy Exon arrays that I need to quantiles normalize at probe level (the reasons for which are complicated!), which means ~6 million probes per sample.

Trying to load the into memory maxes out 32gigs of memory on one of our cluster nodes.

I clearly need to find a way to do this without loading it into memory, would anyone perhaps have a pointer/suggestion?

Thanks!

normalization • 1.7k views
ADD COMMENTlink modified 5.8 years ago by Biostar ♦♦ 20 • written 7.7 years ago by Paul750
6
gravatar for Laurent
7.7 years ago by
Laurent1.6k
Cambridge, UK
Laurent1.6k wrote:

A few suggestions:

  • Aroma affy or xps for on-disk access instead of loading everything into memory,
  • fRMA (frozen RMA) to pre-process single or batches of arrays against precomputed reference probe effects.

Hope this helps.

ADD COMMENTlink written 7.7 years ago by Laurent1.6k
0
gravatar for Malachi Griffith
7.6 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

I also recommend Aroma affy, but you might also consider RMAExpress

ADD COMMENTlink written 7.6 years ago by Malachi Griffith17k
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