Hi all
I'm a bit confused about the difference between the topTable
and toptable
function in limma.
The LogFC in toptable
is equal to the N of topTable
but, for the same gene, I get different p.values and adjusted p.values.
I looked at the limma manual (limma_man file) but it does not specify it.
Can anyone help me clarify this?
Thanks
design <- cbind(N=1,D=c(1,0,1,0,1,1,1,0,1,0))
rownames(design) <- colnames(exprs(eset))
design
fit <- lmFit(eset, design)
fit <- eBayes(fit)
> toptable(fit,adjust="BH",p.value = 0.01,n=10)
logFC t P.Value adj.P.Val B
AFFX-hum_alu_at 11.76798 65.91482 1.606215e-15 1.400083e-11 20.74657
35278_at 10.84990 60.27242 4.245924e-15 1.400083e-11 20.44270
31509_at 10.37781 58.10878 6.315064e-15 1.400083e-11 20.30723
32438_at 10.78534 58.09325 6.333416e-15 1.400083e-11 20.30622
33667_at 10.08915 57.83446 6.647998e-15 1.400083e-11 20.28920
31962_at 11.20030 57.82977 6.653860e-15 1.400083e-11 20.28889
34593_g_at 10.77212 56.13055 9.197907e-15 1.658908e-11 20.17258
33994_g_at 10.36453 55.40145 1.060048e-14 1.672888e-11 20.12012
327_f_at 10.30210 53.83738 1.446484e-14 2.029096e-11 20.00206
35905_s_at 10.57997 52.58897 1.865876e-14 2.355669e-11 19.90205
> topTable(fit,adjust="BH",p.value = 0.01,n=10)
N T AveExpr F P.Value adj.P.Val
AFFX-hum_alu_at 11.76798 0.06389285 11.80632 5466.434 4.500308e-17 5.115957e-13
35278_at 10.84990 0.17770262 10.95652 4630.934 1.109314e-16 5.115957e-13
33667_at 10.08915 -0.05339206 10.05711 4154.550 2.001889e-16 5.115957e-13
32438_at 10.78534 -0.21478303 10.65647 4118.725 2.098423e-16 5.115957e-13
31962_at 11.20030 -0.16281600 11.10261 4107.960 2.128500e-16 5.115957e-13
31509_at 10.37781 -0.49468443 10.08100 3985.109 2.510588e-16 5.115957e-13
33994_g_at 10.36453 0.02694039 10.38070 3848.633 3.034344e-16 5.115957e-13
34593_g_at 10.77212 -0.31503286 10.58310 3802.107 3.241795e-16 5.115957e-13
33322_i_at 11.29747 0.46220237 11.57479 3559.200 4.641677e-16 6.051772e-13
327_f_at 10.30210 -0.20314128 10.18021 3538.194 4.793483e-16 6.051772e-13
You might have a look through the code for
topTable()
, which actually callstoptable()
internally. It's likely thattopTable()
is just overriding some of thetoptable()
defaults.