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 <jholtman@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.xu@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.goslee@gmail.com
> >wrote:
> >
> >> Hi,
> >>
> >> On Wed, Aug 24, 2011 at 2:18 PM, zhenjiang xu <zhenjiang.xu@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]]

