Question: Using raw counts with the 'genie3' algorithm
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gravatar for Tom A
5.7 years ago by
Tom A90
United States
Tom A90 wrote:

Hello BioStars,

Does anyone have any experience running the 'genie3' algorithm in their analysis? (For reference: http://homepages.inf.ed.ac.uk/vhuynht/software.html .)

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! 

Tom 

R rna-seq bioinformatics genie3 • 1.4k views
ADD COMMENTlink written 5.7 years ago by Tom A90
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