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Add data on randomized well population behavior

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efischer
2022-03-02 22:54:17 -06:00
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@@ -264,6 +264,7 @@ Example output:
P-values are calculated *after* BiGpairSEQ matching is completed, for purposes of comparison only, P-values are calculated *after* BiGpairSEQ matching is completed, for purposes of comparison only,
using the (2021 corrected) formula from the original pairSEQ paper. (Howie, et al. 2015) using the (2021 corrected) formula from the original pairSEQ paper. (Howie, et al. 2015)
## PERFORMANCE ## PERFORMANCE
On a home computer with a Ryzen 5600X CPU, 64GB of 3200MHz DDR4 RAM (half of which was allocated to the Java Virtual Machine), and a PCIe 3.0 SSD, running Linux Mint 20.3 Edge (5.13 kernel), On a home computer with a Ryzen 5600X CPU, 64GB of 3200MHz DDR4 RAM (half of which was allocated to the Java Virtual Machine), and a PCIe 3.0 SSD, running Linux Mint 20.3 Edge (5.13 kernel),
@@ -279,6 +280,9 @@ Since this implementation of BiGpairSEQ writes intermediate results to disk (to
with different filtering options), the actual elapsed time was greater. File I/O time was not measured, but took with different filtering options), the actual elapsed time was greater. File I/O time was not measured, but took
slightly less time than the simulation itself. Real elapsed time from start to finish was under 30 minutes. slightly less time than the simulation itself. Real elapsed time from start to finish was under 30 minutes.
As mentioned in the theory section, performance could be improved by implementing a more efficient algorithm for finding
the maximum weighted matching.
## BEHAVIOR WITH RANDOMIZED WELL POPULATIONS ## BEHAVIOR WITH RANDOMIZED WELL POPULATIONS
A series of BiGpairSEQ simulations were conducted using a cell sample file of 3.5 million unique T cells. From these cells, A series of BiGpairSEQ simulations were conducted using a cell sample file of 3.5 million unique T cells. From these cells,
@@ -294,6 +298,7 @@ The well populations of the plates were:
* Five sample plates with each individual well's population randomized, from 1000 to 5000 T cells. (Average population ~3000 T cells/well.) * Five sample plates with each individual well's population randomized, from 1000 to 5000 T cells. (Average population ~3000 T cells/well.)
All BiGpairSEQ simulations were run with a low overlap threshold of 3 and a high overlap threshold of 94. All BiGpairSEQ simulations were run with a low overlap threshold of 3 and a high overlap threshold of 94.
No optional filters were used, so pairing was attempted for all sequences with overlaps within the threshold values.
Constant well population plate results: Constant well population plate results: