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]]
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