or pvalue. padj stands for the adjusted p values.
ID
B
F
L
S
p
padj
003
747
– 0.35
0.17
– 2.08
0.037
0.163
005
0
NA
NA
NA
NA
NA
419
520
0.21
0.1
2.04
0.041
0.176
457
323
0.02
0.15
0.17
0.866
0.962
460
88
– 0.15
0.26
– 0.57
0.567
0.816
938
0
– 1.73
3.49
– 0.5
0.62
NA
xamine data statistics, the summary function was called. The
this call is shown below. Based on the base two logarithm fold
e., LFC and a critical p value 0.1, the model identified 1,564 up-
genes and 1,193 down-regulated genes. It also shows 39% of
ts and 0.84% outliers within the data set.
y(res.table) #summary of results
of 25258 with nonzero total read count
usted p-value < 0.1
> 0 (up) : 1563, 6.2%
< 0 (down) : 1188, 4.7%
liers [1] : 142, 0.84%
counts [2] : 9971, 39%
an count < 10)
see 'cooksCutoff' argument of ?results
] see 'independentFiltering' argument of
ts
summary function has a parameter alpha, which stands for a
value. Its default value is 0.1. When a critical p value was reduced
to 0.01, the new result is shown below, where the DEG numbers
ced.
ary(res.table,alpha=0.01)
25258 with nonzero total read count
ed p-value < 0.01
0 (up) : 851, 3.4%
0 (down) : 586, 2.3%
rs [1] : 142, 0.56%
unts [2] : 9971, 39%