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 _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing