update sleuth (replace edgeR)

workflows/sleuth_differential_expression.R

@@ -4,10 +4,6 @@ library(sleuth)
 library(ggplot2)
 
 # First we need to specify where the kallisto results are stored.
-# If you didn't specify this in your kallisto script, move all kallisto results
-# folders (one for each sample) by GUI or the command line into a new folder called
-# "kallisto_results".
-
 # Begin by storing the base directory of the kallisto results in a variable
 base_dir <- "runs/kallisto_results/"
 
@@ -77,8 +73,8 @@ table(treatment.vs.mock$qval <= 0.01)
 head(treatment.vs.mock)
 
 # <<< challenge excercises >>> #
-# 1. compare the logFC edgeR calculated to that which we did
-# 2. where does the difference comes from? (it's in the edgeR manual)
+# 1. compare the logFC sleuth calculated to that which we did
+# 2. where does the difference comes from?
 
 # now we transfer the result to our compilation data.frame 'dfr'
 # actually, all we really want is the 'false discovery rate' AKA 'q_value'