[Bioc-sig-seq] extract non-zero rows

[Estefania Mancini]

Dear all
I have loaded and analyzed properly 4 454 dataset, corresponding to control and stress samples with their biological replicates.
I would like to know if is possible to filter, in my DGEList  object

-which tags dont have zero in any column,
-which of these tags could be consider "housekeeping" (at least with logFC near 0)
 
The object  DGEList  looks like this:

>dup.data
An object of class "DGEList"
$samples
             group lib.size norm.factors
A8_control control    77953            1
A8_stress   stress   176860            1
mq_control control    98109            1
mq_stress   stress   145839            1
pi_control control   132479            1
pi_stress   stress   142484            1
tj_control control    65827            1
tj_stress   stress   144278            1

I have tried to filter using the suggested function:
>dup.de.filter <- dup.data[rowSums(dup.data$counts) >= 0, ]
or with
>dup.de.filter <- dup.data[rowSums(dup.data$counts) >= 1, ] 
but have no changes at all. I have many rows which 0 and 1 read in some column which should be excluded.

Also:
dup.de.com
An object of class "DGEExact"
$table
                  logConc       logFC   p.value
Glyma13g11940.8 -2.588833  0.26176050 0.7348221
Glyma13g11900.1 -2.875548  0.03020441 0.9688072
Glyma09g24780.1 -3.501041 -0.12108619 0.8754371
Glyma13g12050.1 -3.224648  0.03036675 0.9691009
Glyma13g12070.1 -3.743064  0.14416487 0.8521188
19860 more rows ...

$comparison
[1] "control" "stress" 
$genes
NULL

Thanks in advance,
Estefania