Hi Carol,
I've had trouble with read.table also. It doesn't always read all the
rows and columns. I recommend using read.csv(sep="\t") instead.
Lynn Amon
Martin Morgan wrote:
> carol white <wht_crl at yahoo.com> writes:
>
>
>>
>> t = read.table ("my_file", check.names = FALSE, header = T)
>> gives the same result, modifying duplicate names.
>> Carol
>>
>
> what does sessionInfo() say (i.e., is your R current; is this
> something special to your OS or LOCALE)? Have you done this in a
> 'clean' R session, e.g., starting R from the shell with R --vanilla ?
> And for what it's worth
>
>
>> read.table("~/tmp/tmp.txt", header=TRUE, check.names=FALSE)
>>
> AM2 AM2 AM2 FAL
> 1 2 3 4 5
> 2 1 -1 -3 -2
>
>
>> sessionInfo()
>>
> R version 2.7.1 Patched (2008-07-03 r46033)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics utils datasets grDevices methods base
>
> Martin
>
>
>> --- On Sat, 7/19/08, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>>
>> From: Martin Morgan <mtmorgan at fhcrc.org> Subject: Re:
>> [BioC] problem with read.table To: wht_crl at yahoo.com Cc:
>> bioconductor at stat.math.ethz.ch Date: Saturday, July 19, 2008,
>> 1:52 PM
>>
>>
>> Hi Carol...
>>
>>
>> Carol white <wht_crl at yahoo.com> writes:
>>
>>
>> > Hi,
>>
>> > Although I set check.names to FALSE in read.table, the duplicate names get
>>
>> modified. What should be done in this case?
>>
>> >
>>
>> > the text file to be read by read.table
>>
>> >
>>
>> > AM2 AM2 AM2 FAL
>>
>> > 2 3
>> 4
>>
>> 5
>>
>> > 1 -1 -3 -2
>>
>> >
>>
>> > t = read.table ("my_file", check.names = F, header = T)
>>
>>
>> Maybe spell out TRUE, FALSE (reserved words, cannot be assigned to) to
>>
>> avoid getting the value of variables T, F from your environment??
>>
>>
>> Martin
>>
>>
>> >> t
>>
>> > AM2 AM2.1 AM2.2 FAL
>>
>> >
>>
>> > 2 3 4
>>
>> 5
>>
>> >
>>
>> > 1 -1 -3 -2
>>
>> >
>>
>> > instead of
>>
>> >
>>
>> > AM2 AM2 AM2 FAL
>>
>> >
>>
>> >
>>
>> > 2 3 4
>>
>> 5
>>
>> >
>>
>> >
>>
>> > 1 -1 -3 -2
>>
>> >
>>
>> >
>>
>> > Best,
>>
>> > carol
>>
>> >
>>
>> >
>>
>> >
>>
>> >
>>
>> > [[alternative HTML version deleted]]
>>
>> >
>>
>> > _______________________________________________
>>
>> > Bioconductor mailing list
>>
>> > Bioconductor at stat.math.ethz.ch
>>
>> >
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>>
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>>
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>>
>>
>> --
>>
>> Martin Morgan
>>
>> Computational Biology / Fred Hutchinson Cancer Research Center
>>
>> 1100 Fairview Ave. N.
>>
>> PO Box 19024 Seattle, WA 98109
>>
>>
>> Location: Arnold Building M2 B169
>>
>> Phone: (206) 667-2793
>>
>>
>>
>>
>
>