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

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