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WubingZhang / MAGeCKFlute

Integrative analysis pipeline for pooled CRISPR functional genetic screens
https://github.com/WubingZhang/MAGeCKFlute
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9-square ranking #5

Open cfusterot opened 3 years ago

cfusterot commented 3 years ago

¡Hi!

I've been analyzing CRISPR data using mageckflute (and following the vignette) and I have a question concerning the Squareview results.

After applying the SquareView function, I've retrieved the results table that it generates. This table includes the normalized counts for each analyzed sample, as well as the Difference between control and treatment conditions. There are a few more columns with interesting information: a ranking that orders the genes from negative to positive values, a group column that shows the category determined for each gente (topcenter, midright...) as well as a second ranking column.

My question is: how is this second ranking generated? And how can it be interpreted?

Thanks in advance!

WubingZhang commented 3 years ago

¡Hi!

I've been analyzing CRISPR data using mageckflute (and following the vignette) and I have a question concerning the Squareview results.

After applying the SquareView function, I've retrieved the results table that it generates. This table includes the normalized counts for each analyzed sample, as well as the Difference between control and treatment conditions. There are a few more columns with interesting information: a ranking that orders the genes from negative to positive values, a group column that shows the category determined for each gente (topcenter, midright...) as well as a second ranking column.

My question is: how is this second ranking generated? And how can it be interpreted?

Thanks in advance!

Hi,

Sorry for the late reply. The second rank shows the order of each gene within a specific group, and this column is only for labelling top selected genes.

Best,