Thanks, Jim. quote='' works. And then I found a single quote in each of these lines: 3262 10403 17544 24685 31826 38967
None of them near the position the table got truncated. Why is it? And read.table is a great function. Is it possible for it to give a warning message when the data gets truncated? In my case I almost looked over the truncation... On Thu, Aug 25, 2011 at 11:57 AM, jim holtman <jholt...@gmail.com> wrote: > But did you try the following: > > x <- read.table(...., comment.char = '', quote = '') > > Most cases is that there is a missing quote somewhere in your data. > use a text editor and search for single and double quotes. > > On Thu, Aug 25, 2011 at 11:49 AM, zhenjiang xu <zhenjiang...@gmail.com> > wrote: > > Thanks for your replies. I looked at those lines and didn't spot anything > > unusual. > > > >> tail(a) > > test_id gene_id gene locus sample_1 sample_2 status > > 21418 tY(GUA)J1 - SUP7 chr10:354243-354332 air1rrp6 air2rrp6 OK > > 21419 tY(GUA)J2 - SUP4 chr10:542955-543044 air1rrp6 air2rrp6 OK > > 21420 tY(GUA)M1 - SUP5 chr13:168794-168883 air1rrp6 air2rrp6 OK > > 21421 tY(GUA)M2 - SUP8 chr13:837927-838016 air1rrp6 air2rrp6 OK > > 21422 tY(GUA)O - SUP3 chr15:288191-288280 air1rrp6 air2rrp6 OK > > 21423 tY(GUA)Q - - chrmt:70823-70907 air1rrp6 air2rrp6 > OK > > value_1 value_2 ln.fold_change. test_stat p_value q_value > > significant > > 21418 0.00000 0.0000 0.000000 0.00000 1.000000 1.011650 > > no > > 21419 0.00000 0.0000 0.000000 0.00000 1.000000 1.011480 > > no > > 21420 0.00000 0.0000 0.000000 0.00000 1.000000 1.011500 > > no > > 21421 0.00000 0.0000 0.000000 0.00000 1.000000 1.011520 > > no > > 21422 0.00000 0.0000 0.000000 0.00000 1.000000 1.011550 > > no > > 21423 6.68356 10.7397 0.474301 -1.08614 0.277417 0.455917 > > no > > > > > > tY(GUA)J1 - SUP7 chr10:354243-354332 rrp6 air1rrp6 > > OK 0 0 0 0 1 1.00404 no > > tY(GUA)J2 - SUP4 chr10:542955-543044 rrp6 air1rrp6 > > OK 0 0 0 0 1 1.00497 no > > tY(GUA)M1 - SUP5 chr13:168794-168883 rrp6 air1rrp6 > > OK 0 0 0 0 1 1.00492 no > > tY(GUA)M2 - SUP8 chr13:837927-838016 rrp6 air1rrp6 > > OK 0 0 0 0 1 1.00488 no > > tY(GUA)O - SUP3 chr15:288191-288280 rrp6 air1rrp6 > > OK 0 0 0 0 1 1.00485 no > > tY(GUA)Q - - chrmt:70823-70907 rrp6 air1rrp6 > > OK 4.49644 6.68356 0.396365 -0.766052 0.443645 > > 0.634724 no > > 15S_rRNA - 15S_RRNA chrmt:6545-8194 WT air2rrp6 > > OK 2288.88 711.697 -1.16817 2.78772 0.00530801 > > 0.0167772 yes > > 21S_rRNA - 21S_RRNA chrmt:58008-62447 WT > > air2rrp6 OK 4134.59 1927.04 -0.7634 1.58991 0.111855 > > 0.22339 no > > ETS1-1 - ETS1-1 chr12:457732-458432 WT air2rrp6 > OK > > 3258.97 1114.76 -1.07277 2.91211 0.00359 0.0121587 > yes > > ETS1-2 - ETS1-2 chr12:466869-467569 WT air2rrp6 > OK > > 3258.97 1114.76 -1.07277 2.91211 0.00359 0.0121597 > yes > > > > > > On Wed, Aug 24, 2011 at 2:34 PM, Sarah Goslee <sarah.gos...@gmail.com > >wrote: > > > >> Hi, > >> > >> On Wed, Aug 24, 2011 at 2:18 PM, zhenjiang xu <zhenjiang...@gmail.com> > >> wrote: > >> > Hi R users, > >> > > >> > I was using read.table to read a file. The data.fame looked alright, > but > >> I > >> > found not all rows are read by the read.table. What's wrong with it? > It > >> > didn't give me any warning or error messages. Why the data are > truncated? > >> > Thanks. > >> > > >> > $ wc -l all/isoform_exp.diff > >> > 42847 all/isoform_exp.diff > >> > > >> >> a=read.table('all/isoform_exp.diff', header=T, sep='\t') > >> >> nrow(a) > >> > [1] 21423 > >> > >> This is a common problem. You need to take a look at the last row that > >> was imported, and the rows around 21423 in the original file. > >> > >> Common causes include stray single or double quotation marks, and > >> other special characters in your file like the default comment.char # > >> > >> Sarah > >> -- > >> Sarah Goslee > >> http://www.functionaldiversity.org > >> > > > > > > > > -- > > Best, > > Zhenjiang > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > > > -- > Jim Holtman > Data Munger Guru > > What is the problem that you are trying to solve? > -- Best, Zhenjiang [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.