[R] Weird read.table error? (line `n' did not have `m' elements)

[Peng Yu]

Here are the outputs.

> strsplit(scanned_file[5205],'\t')[[1]]
 [1] "6836237"
 [2] "8.146431"
 [3] "8.197432"
 [4] "8.156005"
 [5] "7.98905"
 [6] "8.327593"
 [7] "7.673796"
 [8] "8.119687"
 [9] "8.077252"
[10] "Asap1 "
[11] "NM_010026 "
[12] "RefSeq "
[13] "Mus musculus ArfGAP with SH# domain, ankyrin repeat and PH
domain1 (Asap1), mRNA. "
[14] "FALSE"
[15] "GO:0032312 "
[16] "regulation of ARF GTPase activity "
[17] "GO:0005737  // GO:0016020 "
[18] "cytoplasm  // membrane "
[19] "GO:0005096  // GO:0005515  // GO:0008060  // GO:0008270  //
GO:0046872 "
[20] "GTPase activator activity  // protein binding  // ARF GTPase
activator activity  // zinc ion binding  // metal ion binding "
[21] "---"
[22] "---"
> scanned_file[5205]
[1] "6836237\t8.146431\t8.197432\t8.156005\t7.98905\t8.327593\t7.673796\t8.119687\t8.077252\tAsap1
\tNM_010026 \tRefSeq \tMus musculus ArfGAP with SH# domain, ankyrin
repeat and PH domain1 (Asap1), mRNA. \tFALSE\tGO:0032312 \tregulation
of ARF GTPase activity \tGO:0005737  // GO:0016020 \tcytoplasm  //
membrane \tGO:0005096  // GO:0005515  // GO:0008060  // GO:0008270  //
GO:0046872 \tGTPase activator activity  // protein binding  // ARF
GTPase activator activity  // zinc ion binding  // metal ion binding
\t---\t---"


On Mon, Sep 21, 2009 at 9:34 PM, Gabor Grothendieck
<ggrothendieck at gmail.com> wrote:
> Its highly unusual to use xls as the extension for a text file.
> Use something more suggestive.
>
> print out the line in question.  For example, note that scan
> and read.table have different defaults for the comment character,
> namely, none and #.
>
> On Mon, Sep 21, 2009 at 10:23 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>> On Mon, Sep 21, 2009 at 9:12 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>>> Hi,
>>>
>>> I have the following commands. It says line 5205 does not have 22
>>> elements. But I use my 'vim' checked that line in the file. It has 22
>>> fields. Can somebody let me know how to further debug this case?
>>>
>>> Regards,
>>> Peng
>>>
>>>> annotation = read.table("../EC_results/Juan_15wks_gene_core.xls", header=T, sep='\t',quote='')
>>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>>>  line 5204 did not have 22 elements
>>>> annotation = count.fields("../EC_results/Juan_15wks_gene_core.xls", sep='\t',quote='')
>>>> which(annotation!=22)
>>> [1] 5205
>>>
>>
>>
>> I also run the following command to test, which confirms that line
>> 5205 has 22 elements. Is it a bug in read.table?
>>
>>> scanned_file = scan("../EC_results/Juan_15wks_gene_core.xls", what=character(),sep='\n',quote='')
>> Read 23333 items
>>> length(strsplit(scanned_file[5205],'\t')[[1]])
>> [1] 22
>>
>> Regards,
>> Peng
>>
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>>
>