Thanks for the suggestion. I guess that's the only thing I could do On Fri, Aug 26, 2011 at 4:22 AM, Petr PIKAL <petr.pi...@precheza.cz> wrote:
> Hi > > > > > 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... > > When I read in some big data I usually do > > str(data) > > which tells me if there is some problem with data types (conversion of > numeric to factor due to any problematic item) > > and/or > > dim(data) > > to see that size is as expected. > > Regards > Petr > > > > > 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. > > -- 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.