No problem - I apologize for the lack of clarity.
>>> import rpy2.robjects as robjects
>>> r = robjects.r
>>> wilcox = robjects.r['wilcox.test']
>>> vec1 = [1,2,3,4,5]
>>> vec2 = [4,5,6,7,8]
>>> rvec1 = robjects.FloatVector(vec1)
>>> rvec2 = robjects.FloatVector(vec2)
>>> address = wilcox(rvec1, rvec2)
Warning message:
In wilcox.test.default(c(1, 2, 3, 4, 5), c(4, 5, 6, 7, 8)) :
cannot compute exact p-value with ties
>>> address
<RVector - Python:0x6c9e18 / R:0xda4608>
>>> print address
>>>
Wilcoxon rank sum test with continuity correction
data: c(1, 2, 3, 4, 5) and c(4, 5, 6, 7, 8) #herein
likely lies the problem if it's big
W = 2, p-value = 0.03558
alternative hypothesis: true location shift is not equal to 0
#right here is the problem that I ran into. If I convert address to a
string and split it to get out the p value,
#funny things start happening once the aggregate vector length (e.g.
both of them) is about 1500
#i think it is because R returns the primary data as illustrated
above, and once that data line gets out to 1500 or
#so converting the address to a string returns only one of the
following four lines, and if it's the fourth line, that gets
#truncated
#but inside the R documentation for the wilcox test (below), i found
that besides the above output, which i am
#used to seeing, R is storing the following values as a list:
1. statistic
the value of the test statistic with a name describing it.
2. parameter
the parameter(s) for the exact distribution of the test statistic.
3. p.value
the p-value for the test.
4. null.value
the location parameter mu.
5. alternative
a character string describing the alternative hypothesis.
6. method
the type of test applied.
7. data.name
a character string giving the names of the data.
8. conf.int
a confidence interval for the location parameter. (Only present if
argument conf.int = TRUE.)
9. estimate
an estimate of the location parameter. (Only present if argument
conf.int = TRUE.)
#so directly extracting what you need from the stored variable seems
to do the trick:
>>> pval = str(address[2])
>>> pval
'[1] 0.03557883'
>>> pvalactual = float(pval[4:])
>>> pvalactual
0.035578829999999999
#totally easy in hindsight, which is the way i guess most things are
#but i hope this is helpful to other rookies who run into the problem
On Apr 4, 2009, at 5:47 AM, Laurent Gautier wrote:
> Joel,
>
> Good that you solved your issue.
> However, I am not certain of what you mean by "extracting the
> required object directly from the address rather than first
> converting the address to a string".
>
> Self-contained examples often constitute a very efficient way to
> demonstrate the problem when requesting help from the list.
>
>
> L.
>
>
>
>
>
> Joel Neilson wrote:
>> although i still don't understand what's happening and why, this
>> problem went away if i extracted the required object directly from
>> the address rather than first converting the address to a string
>> or list and then indexing out what i wanted.
>> i'm new to both python and computer science in general, so if this
>> is obvious to everyone on the list i apologize. however, it seems
>> that the others have run into analogous problems with long R
>> outputs (see: '[Rpy] R console: long output' thread) and it was
>> not obvious to me upon reading these threads precisely where the
>> problem was occurring. now i know and hopefully this is useful
>> information.
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> rpy-list mailing list
>> rpy-list@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rpy-list
>
Joel R. Neilson, Ph.D.
Research Scientist/Sharp Lab
Koch Institute for Integrative Cancer Research
Massachusetts Institute of Technology
40 Ames Street, E17-528
Cambridge, MA 02139
t: 617.253.6457
f: 617.253.3867
jneil...@mit.edu
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