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fix typo

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eugenefischer
2022-10-01 16:11:32 -05:00
parent 98ce708825
commit 2eede214c0
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readme.md
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@@ -458,7 +458,7 @@ Example output:
---
**NOTE: The p-values in the sample output abpve are not used for matching**—they aren't part of the BiGpairSEQ algorithm at all.
**NOTE: The p-values in the sample output above are not used for matching**—they aren't part of the BiGpairSEQ algorithm at all.
P-values (if enabled in the interactive menu options or by using the -pv flag in the command line) are calculated *after*
BiGpairSEQ matching is completed, for purposes of comparison with pairSEQ only, using the (corrected) formula from the
original pairSEQ paper. (Howie, et al. 2015) Calculation of p-values is off by default to reduce processing time.
@@ -519,7 +519,7 @@ This and several other tests indicate that BiGpairSEQ treats a sample plate with
roughly as though it had a constant well population equal to the plate's average well population.
### EXPERIMENTS FROM THE 2015 pairSEQ PAPER
#### Experiment 1
#### Experiment 1 (Need to be re-tried with different lambda values.)
This simulation was an attempt to replicate the conditions of experiment 1 from the 2015 pairSEQ paper: a matching was found for a
96-well sample plate with 4,000 T cells/well comprising ~11,900 TCRAs and TCRBs, taken from a sample of 8,400,000
distinct cells with an exponential frequency distribution (lambda 0.6). The sequence dropout rate was 10%, as the analysis
@@ -544,6 +544,7 @@ Note that the frequency distribution of T cell clones in this simulation is only
#### Experiment 2
## TODO
* ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE