User: Jeff Granja

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Posts by Jeff Granja

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Comment: C: DESEq2 Large Memory When Parallel
... In this case there is about ~25 Types with ~3 Patients (~75 Patient_Type) with 2+ replicates so in total ~150 samples. ...
written 29 days ago by Jeff Granja0
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Comment: C: DESEq2 Large Memory When Parallel
... Sure. So the datasets that cause the main problems definitely have lots of coefficients (50+). For this design in particular we have lots of cell types from mulitple donors and the questions we are interested in is the difference between the cell types as a whole and across individuals. For each in ...
written 29 days ago by Jeff Granja0
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Comment: C: DESEq2 Large Memory When Parallel
... I have been doing approximately that right as we speak. I have been using 8 cores ~60k rows (thresholding) and it took around ~8 hours when 12 cores ~400k rows was about ~24 hours (with ~300 GB of RAM usage). The memory usage scales with the size of the counts 8 cores 60k rows uses 3-4GB per thread ...
written 29 days ago by Jeff Granja0
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Comment: C: DESEq2 Large Memory When Parallel
... Normally 16-24 ...
written 29 days ago by Jeff Granja0
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Comment: C: DESEq2 Large Memory When Parallel
... The operating system is Ubuntu 14.04.1 LTS. ...
written 29 days ago by Jeff Granja0
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Comment: C: DESEq2 Large Memory When Parallel
... Hi, I guess I mistook maybe that the size of the object being big itself but the object.size of dds is 24554008 bytes, the way i run BiocParallel is (threads i normally set to 16-24) library(BiocParallel) register(MulticoreParam(threads)) #threads normally 16-24 print("Garbage Collecting") gc() ...
written 29 days ago by Jeff Granja0
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DESEq2 Large Memory When Parallel
... I have a direct question about DESeq2's memory handling. I have come to really enjoy DESeq2 for ATAC-Seq and it is really well documented etc. The problem is matrices can get quite large in rows which slows down DESeq a lot. This is why the parallelism of DESeq is quite useful. I was curious if ther ...
deseq2 written 4 weeks ago by Jeff Granja0 • updated 29 days ago by Michael Love15k
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Comment: C: Using the "listValues" argument of DESEQ in multiple group comparisons
... Thanks exactly what i was looking for! ...
written 10 weeks ago by Jeff Granja0

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