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4 hours ago by

China/Xiamen/Xiamen University

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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4 hours ago
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xpan0



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