When I use "mageck count", I get a hesitation that lfc for positive selection pull from the negative selection cutoffs. This is most apparent when the output table is sorted by positive selection.
In 2017, the author answered a similar question that solved through updating to the latest version.But my software version is 0.5.9.2 which is much higher than the version at that time.
I observed the gene SLC22A17 's sgRNA have two FALSE and one TRUE in high_in_treatment, and the TRUE 's pvalue is the most significant. I guess it is because the TRUE sgRNA influenced the rank in the RRA algorithm. But what kind of selection should I define for gene SLC22A17. Is there any other better solution.Thanks for help.
Table 1. gene_summary. [The "pos|lfc" of gene which rank is 19/26/29 is negative ]
| id | num | pos|score | pos|p-value | pos|fdr | pos|rank | pos|goodsgrna | pos|lfc |
|---|---|---|---|---|---|---|---|
| SLC35A1 | 3 | 1.77E-09 | 2.40E-07 | 0.002475 | 1 | 3 | 9.743 |
| VMA21 | 3 | 2.38E-08 | 2.40E-07 | 0.002475 | 2 | 2 | 6.5683 |
| JAG1 | 3 | 1.71E-05 | 5.53E-05 | 0.315594 | 3 | 3 | 3.1071 |
| SLC22A17 | 3 | 0.00031586 | 0.00092729 | 0.88592 | 19 | 1 | -6.5016 |
| YPEL2 | 3 | 0.00046162 | 0.0013556 | 0.88592 | 26 | 1 | -2.0106 |
| IKZF1 | 3 | 0.00051021 | 0.0014768 | 0.88592 | 29 | 1 | -5.9793 |
Table 2. sgRNA_summary. [Gene SLC22A17 which rank is 19 ]
| sgrna | Gene | control_count | treatment_count | control_mean | treat_mean | LFC | control_var |
|---|---|---|---|---|---|---|---|
| HGLibA_44559 | SLC22A17 | 1.4111 | 0/1317 | 1.4111 | 658.5 | 8.0955 | 8.67E+05 |
| HGLibA_44557 | SLC22A17 | 90.313 | 0/0 | 90.313 | 0 | -6.5127 | 0 |
| HGLibA_44558 | SLC22A17 | 89.607 | 0/0 | 89.607 | 0 | -6.5016 | 0 |
| adj_var | score | p.low | p.high | p.twosided | FDR | high_in_treatment | |
| 116.72 | 60.82 | 1 | 0 | 0 | 0 | TRUE | |
| 20740 | 2.8924 | 0.0019116 | 0.99809 | 0.0038231 | 0.018508 | FALSE | |
| 20538 | 2.8902 | 0.0019248 | 0.99808 | 0.0038495 | 0.018508 | FALSE |
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