On Jul 18, 2011, at 11:10 AM, Andrea Franceschini wrote:
Dear Philipp,
You were right,
thankyou very much.
Effectively the second read.table didn't work (probably because of the
strange characters).
From my point of view this is a very bad R bug.
When I read this I thought it was an example of a young person just
starting their education exhibiting Piaget's "preoperational" stage
when applied to the task of learning a computer language.
"the child begins to use symbols to represent objects. Early in this
stage he also personifies objects. [snipped] His thinking is
influenced by fantasy -- the way he'd like things to be -- and he
assumes that others see situations from his viewpoint."
[Copied from a webpage for grade school teachers: http://www2.honolulu.hawaii.edu/facdev/guidebk/teachtip/piaget.htm
]
But when I do a search in PubMed, I find that you may be an
established researcher, so I thing the onus is now on you to
demonstrate how R's behavior is different than the documented design
goals for the read.table function.
I precisely inserted the "\t" separator in the read table command,
hence I would expect that everything is working.
How can I make it work ???
I thought Pagel already gave you the answer, but your response is too
general to be sure. What exactly did you find and can you provide a
minimal code and data example that illustrates how read.table is
acting in any way different than the documentation describes?
--
David.
Effectively there are several ' (i.e. apostrophe) characters in the
file. I guess are those that confuse R
Thankyou very much,
Best Regards,
Andrea
On Mon, Jul 18, 2011 at 4:32 PM, Philipp Pagel <p.pa...@wzw.tum.de>
wrote:
On Mon, Jul 18, 2011 at 04:00:29PM +0200, Andrea Franceschini wrote:
I use version 13 of R in OSX (downloaded and installed less than 1
year ago).
Probably 2.13 ...
[...] code omitted
The first lines are OK (i.e. 14 columns, like the dataframe),
while at
a certain point I get lines with only 3 columns !!!
The bad lines that contain only 3 columns have the name and the
description of the gene (i.e. the content of the file that I merged
with).
Besides, these strange lines also get repeated (see the bottom).
I havent't carefully analyzed your code so I may be wrong but my
guess for
all "weird behaviour of gene related data.frames" problems is this:
Gene descriptions love to contain things like "Foo 5' obfuscation
factor". Note the "'" in the description which read.table will
happily interpret as a quotation mark and eat lots of rows until it
happens to encouter a closing counterpart. This leads to all kinds of
funny results. So I bet your problem is not in write.table but in
reading the data. Have a closer look at your data frame: are you
really getting the expected number of observations in the merged
data.frame? Are the rows in question really ok in the data frame? If
my guess is correct you should be able to fix your problem by
including quote="" in both your read.table commands.
If it doesn't, also try comment.char="" - another popular source of
problems.
cu
Philipp
--
Dr. Philipp Pagel
Lehrstuhl für Genomorientierte Bioinformatik
Technische Universität München
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany
http://webclu.bio.wzw.tum.de/~pagel/
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