gravatar for grd

2 hours ago by

France

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?

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2 hours ago
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grd0



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