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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* 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 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. 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. roughly as though it had a constant well population equal to the plate's average well population.
### EXPERIMENTS FROM THE 2015 pairSEQ PAPER ### 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 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 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 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 #### Experiment 2
## TODO ## TODO
* ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE * ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE