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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