diff --git a/readme.md b/readme.md index 31cb0d3..98e8349 100644 --- a/readme.md +++ b/readme.md @@ -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