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Commit 7a9114be authored by Christian Arnold's avatar Christian Arnold
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Documentation updates

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......@@ -30,8 +30,7 @@ par.l = list()
# Hard-coded parameters
par.l$verbose = TRUE
par.l$FDR_threshold = c(0.001, 0.01, 0.05,0.1,0.2)
par.l$probsThreshold = c(0.01, 0.99)
par.l$probsThreshold = c(0.05, 0.95)
par.l$probsThreshold = c(0, 1)
par.l$expressionThreshold = 2
par.l$cohensDThreshold = 0.1
par.l$classes_CohensD = c("small", "medium", "large", "very large")
......@@ -264,21 +263,6 @@ CME.delta = estimates[2]
# as seen in Figure 6.1a, can derail central matching. The MLE method is more stable, but pays the price of possibly increased bias.
# 2. Should the variance associated with this weighted.mean T stat value be based on the variance of the T stat scores, the variance of the mean, or both?
# 3. Why not estimate the SD of the distribution directly, without the need to provide manual variance estimations? Because then each weigted mean value
# is treated as if it came from the same population?
# 4. library(Hmisc) -> wtd.var(x, weights)
# 5 . Variance estimation is based on before the centralization, is this correct? Yes, independent
# 6. Is centralization actually correct at all since the scores come from a different population? Yes, if assumed they come from a normal distribution
# NEW: Estimate variance of T score estimate with Welch corrected df (test$parameter)
# READ http://genomicsclass.github.io/book/pages/t-tests_in_practice.html
output.global.TFs$weighted_Tstat_centralized = output.global.TFs$weighted_Tstat - MLE.delta
output.global.TFs$variance = as.numeric(output.global.TFs$variance)
......
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