[BioC] Question about amount of diff expressed genes in fit using a design matrix with intercept

[Belisa Santos [guest]]

Hello everybody, 

    I have used a design matrix with a control as intercept. When I fit the matrix with my RMA normalized expression set, do eBayes, and then ask for a topTable:
topTable(fit, adjust="BH", p.value=1e-5, lfc=1, number=Inf)
I get the same number of genes as I have input (54675)... and the lowest adjusted p-value is e-29... Now it cannot be the case where ALL my genes are differentially expressed between control and treatments....

I am missing something? The intercept functions as a "contrast", right? Is this common?  Could I be doing something wrong? Please help me...

Thank you in advance for you kind help. All the best, 

Belisa


 -- output of sessionInfo(): 

# Code I am using, 
cel<-ReadAffy

expression_set <- rma(cel)

fit <- lmFit(expression_set, design.ctrl_intercept)
fit <- eBayes(fit)
topTable(fit, adjust.method="BH", p.value=1e-5, lfc=1, number=Inf)

# My design matrix

   ctrl0 B1.ctrl BT1.ctrl BI1.ctrl BTI1.ctrl B2.ctrl BT2.ctrl BI2.ctrl BTI2.ctrl B3.ctrl BT3.ctrl BI3.ctrl BTI3.ctrl B7.ctrl BT7.ctrl BI7.ctrl BTI7.ctrl
1      1  0   0   0    0  0   0   0    0  0   0   0    0  0   0   0    0
2      1  0   0   0    0  0   0   0    0  0   0   0    0  0   0   0    0
3      1  0   0   0    0  0   0   0    0  0   0   0    0  0   0   0    0
4      1  0   0   0    0  0   0   0    0  0   0   0    0  0   0   0    0
5      1  0   0   0    0  0   0   0    0  0   0   0    0  0   0   0    0
6      1  0   0   0    0  0   0   0    0  0   0   0    0  0   0   0    0
7      1  1   0   0    0  0   0   0    0  0   0   0    0  0   0   0    0
8      1  1   0   0    0  0   0   0    0  0   0   0    0  0   0   0    0
9      1  1   0   0    0  0   0   0    0  0   0   0    0  0   0   0    0
10     1  0   1   0    0  0   0   0    0  0   0   0    0  0   0   0    0
11     1  0   1   0    0  0   0   0    0  0   0   0    0  0   0   0    0
12     1  0   1   0    0  0   0   0    0  0   0   0    0  0   0   0    0
13     1  0   0   1    0  0   0   0    0  0   0   0    0  0   0   0    0
14     1  0   0   1    0  0   0   0    0  0   0   0    0  0   0   0    0
15     1  0   0   1    0  0   0   0    0  0   0   0    0  0   0   0    0
(...)
52     1  0   0   0    0  0   0   0    0  0   0   0    0  0   0   0    1
53     1  0   0   0    0  0   0   0    0  0   0   0    0  0   0   0    1
54     1  0   0   0    0  0   0   0    0  0   0   0    0  0   0   0    1

--
Sent via the guest posting facility at bioconductor.org.