mageck positive alphamean/median lfc reported based on negative selection
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Entering edit mode
19 months ago
xpan • 0

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 ]

idnumpos|scorepos|p-valuepos|fdrpos|rankpos|goodsgrnapos|lfc
SLC35A131.77E-092.40E-070.002475139.743
VMA2132.38E-082.40E-070.002475226.5683
JAG131.71E-055.53E-050.315594333.1071
SLC22A1730.000315860.000927290.88592191-6.5016
YPEL230.000461620.00135560.88592261-2.0106
IKZF130.000510210.00147680.88592291-5.9793

Table 2. sgRNA_summary. [Gene SLC22A17 which rank is 19 ]

sgrnaGenecontrol_counttreatment_countcontrol_meantreat_meanLFCcontrol_var
HGLibA_44559SLC22A171.41110/13171.4111658.58.09558.67E+05
HGLibA_44557SLC22A1790.3130/090.3130-6.51270
HGLibA_44558SLC22A1789.6070/089.6070-6.50160
adj_varscorep.lowp.highp.twosidedFDRhigh_in_treatment
116.7260.821000TRUE
207402.89240.00191160.998090.00382310.018508FALSE
205382.89020.00192480.998080.00384950.018508FALSE
mageck sgRNA GeCKO • 732 views
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I noticed the parameter "--gene-lfc-method" of MaGeCK has the options "alphamedian/alphamean".When set this parameter, MaGeCK will only use the gene which fold change were negative to selected negative gene. Perhaps, this method of circumventing the opposite trend sgRNA may be made sense.

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