Entering edit mode
4.1 years ago
grd
•
0
Hi all,
I am doing a "two class unpaired" differential expression analysis using samr:
samr.obj <- samr(data1,
resp.type = "Two class unpaired",
assay.type = "array",
nperms=1000,
center.arrays=TRUE,
testStatistic = "standard", # student t-test
random.seed=42)
delta.table <- samr.compute.delta.table(samr.obj)
print(delta.table[,1:6])
I obtain a list of statistically significant negative genes (that is: genes whose expression is higher in group 1 than group 2):
Gene.ID Score.d. Fold.Change
1 g01 -5.469 0.102
2 g02 -3.952 0.205
3 g03 -3.131 -0.004
4 g04 -2.902 0.209
5 g05 -2.258 0.408
Anyway, I do not understand that negative Fold Change at line 3
. Data is not log2-transformed.
How does samr actually compute Fold Change?