Read Gabor's advice more closely: Especially unlucky "#" (hint, hint)
13.
On Sep 21, 2009, at 11:08 PM, Peng Yu wrote:
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
<ggrothendi...@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...@gmail.com>
wrote:
On Mon, Sep 21, 2009 at 9:12 PM, Peng Yu <pengyu...@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
______________________________________________
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.
______________________________________________
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.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
______________________________________________
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.
