Using raw counts with the 'genie3' algorithm
Entering edit mode
9.0 years ago
Tom A ▴ 110

Hello BioStars,

Does anyone have any experience running the 'genie3' algorithm in their analysis? (For reference:

If so, I am trying to decipher whether I can use raw RNA-Seq counts as my input, or if the input should be normalized and fold change (exp/ctrl) calculated. The reason I ask is that when running it with normalized fold change values, I run into errors due to the 'Inf' values in my data. I can circumvent the issue by commenting out the

expr.matrix <- apply(expr.matrix, 2, function(x) { (x - mean(x)) / sd(x) } )

line of the code (I work in R), or when I simply substitute the 'Inf' value for a large number (ex: 50,000), but I am not sure that this is a valid approach.

Thanks in advance!


R RNA-Seq genie3 • 2.1k views

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