Hello Davis, Yes, you have explained the issue and now it is fixed. Many thanks! Sridhara On Wed, Feb 16, 2011 at 11:03 PM, Davis McCarthy <dmccarthy@wehi.edu.au>wrote: > Hi Sridhara > > This is not a problem as such, your issue will hopefully be solved with a > little more explanation of how readDGE() (an edgeR function) and > read.delim() (a base R function) work. > > You will see in the documentation for readDGE() > > ?readDGE > that it accepts several named arguments and an argument '...' which > indicates that any further arguments are passed to read.delim(). In your > example from the User's Guide, the arguments 'skip=5' and 'comment.char="!"' > are arguments that are passed to read.delim(). 'skip=x' skips the first x > lines of each file being read in. 'comment.char="!"' skips (does not read > in) any line beginning with '!'. These extra arguments were needed for the > dataset used in the example in the User's Guide, but are not needed > generally. That, perhaps, is not clear in the User's Guide (an overhaul > thereof is on my TODO list). > > You are missing one line even when you set 'skip=0' because one of the > defaults for read.delim() is 'header=TRUE', which means that by default > read.delim() assumes the first line of your file is a header and does not > read it into the table in R. Unsurprisingly, you can change this behaviour > by setting 'header=FALSE'. > > See > > ?read.delim > for more information about the use of read.delim. > > For your example, the call > > d <- readDGE(targets, header=FALSE) > should get all of your data read into a DGEList object in your R session. > > Hope that explains why your issue was arising and fixes it so that you can > proceed with your analysis. > > Best wishes > Davis > > > > > > On Feb 17, 2011, at 1:47 PM, Sridhara Gupta Kunjeti wrote: > > > 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 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -------------------------------------------------------------------- ---- > Davis J McCarthy > Research Technician > Bioinformatics Division > Walter and Eliza Hall Institute of Medical Research > 1G Royal Parade, Parkville, Vic 3052, Australia > dmccarthy@wehi.edu.au > http://www.wehi.edu.au > > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:20}}