Hello,
I was using the edgeR for Reading in the data and creating DGEList objects.
I followed the instruction as described in edgeR user guide.

I noticed that not all the entries in the files were loaded into R,
especially first few entries.
The steps / codes that I used were:

step 1. created a plane text with the following information:
files    group    description
F0a    PhyP18B1.txt    PhyP18    Phytophthora phaseoli
F0b    PhyP18B2.txt    PhyP18    Phytophthora phaseoli
P3a    PPLB3dpiB1.txt    PPLB3dpi    Phytophthora phaseoli
P3b    PPLB3dpiB2.txt    PPLB3dpi    Phytophthora phaseoli

step 2.
> setwd("C:/Users/SRIDHARA/Documents/test/bowtie/0_mismatch")
> targets <- read.delim(file = "targets.txt", stringsAsFactors = FALSE)
> targets
                     files    group           description
F0a   PhyP18B1.txt   PhyP18 Phytophthora phaseoli
F0b   PhyP18B2.txt   PhyP18 Phytophthora phaseoli
P3a PPLB3dpiB1.txt PPLB3dpi Phytophthora phaseoli
P3b PPLB3dpiB2.txt PPLB3dpi Phytophthora phaseoli
P6a PPLB6dpiB1.txt PPLB6dpi Phytophthora phaseoli
P6b PPLB6dpiB2.txt PPLB6dpi Phytophthora phaseoli

Step 3.
> d <- readDGE(targets, skip = 5, comment.char = "!")
> d
An object of class "DGEList"
$samples
             files    group           description lib.size norm.factors
F0a   PhyP18B1.txt   PhyP18 Phytophthora phaseoli  2442435            1
F0b   PhyP18B2.txt   PhyP18 Phytophthora phaseoli  7355562            1
P3a PPLB3dpiB1.txt PPLB3dpi Phytophthora phaseoli   474592            1
P3b PPLB3dpiB2.txt PPLB3dpi Phytophthora phaseoli    13778            1
P6a PPLB6dpiB1.txt PPLB6dpi Phytophthora phaseoli  3280812            1
P6b PPLB6dpiB2.txt PPLB6dpi Phytophthora phaseoli  3906611            1

$counts

                                 F0a F0b P3a P3b P6a P6b
PITG_23029 | Pi Crinkler (CRN) family protein, pseudogene (1794 nt) 170
109   0     0     12   8
PITG_14644 | Pi AMP-binding enzyme, putative (2568 nt)                   5
  46    0     0     44  44
PITG_09824 | Pi metalloprotease family M12A, putative (1230 nt)       7
17    1     0     33   8

Here it first five entries were removed,
when I use the following codes:
> d <- readDGE(targets, skip = 0, comment.char = "!")
OR
> d <- readDE(targets)
I noticed that first entry is removed. There is first entry with counts,
which I wanted to be taken into account for the DGE.

I was wondering if I am doing something wrong, or is there a way to fix this
problem?

Any comments or suggestions will be appreciated.

Many thanks in advance,
Sridhara

-- 
Sridhara G Kunjeti
PhD Candidate
University of Delaware
Department of Plant and Soil Science
email- sridhara@udel.edu
Ph: 832-566-0011

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