A total of 4 different pvalues are provided viz, raw p-value, -log10 pvalue, Holm-Bonferroni adjusted p-value and the FDR value. And a impact score.
Which value should be considered in my case below to get significant pathways? And what should be the threshold cut off?
Sal Mangiafico
I would use the raw p-values, with a cutoff of alpha = 0.05. This is appropriate for identifying likely significant tests across many, as if in an initial screening.
Unless I misunderstand something of what you are doing.
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