Hi all
Newbie question.
I've generated a very simple script to process gene expression data
from mysql output.
One of the things I'm trying to do is feed vectors that I generate in
this script into a wilcoxon test through rpy2, and collecting the p
value as output.
Some of the vectors are
R is complaining because you handed the 'oneway' function a single
string parameter.
Instead of
oneway = robjects.r['oneway.test']
test = oneway("values ~ ind, data=d, var.equal=TRUE")
try this:
test = robjects.r['oneway.test(values ~ ind, data=d, var.equal=TRUE)']
or
oneway = robjects.r[
On Thu, Apr 9, 2009 at 10:08 AM, Warnes, Gregory R.
wrote:
> Instead of
> oneway = robjects.r['oneway.test']
> test = oneway("values ~ ind, data=d, var.equal=TRUE")
> try this:
> test = robjects.r['oneway.test(values ~ ind, data=d, var.equal=TRUE)']
Typo: should use () here, not []:
test = r
I have an R function that returns a list of Matrices and Vectors.
I've been processing the return list like:
rpyRV = rpy2.robjects.r.someFunc()
for property,rObj in zip([i for i in rpyRV.getnames()],[i for i in rpyRV]):
# do stuff with results
On my development box (64 bit, dual XEON) everythi
Sorry, forgot the backtrace -->
(gdb) run test.py
Starting program: /usr/bin/python test.py
(no debugging symbols found)
[Thread debugging using libthread_db enabled]
[New Thread 46912506825472 (LWP 7658)]
[New Thread 1082132832 (LWP 7675)]
[New Thread 1090525536 (LWP 7676)]
Program received sign
Many thanks!
I see now how this works.
Best,
Juls
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Hi all,
I'm somewhat new to Rpy, and trying to use the R random forests
package from Python, and depending on the type it receives for one
variable it switches behaviour. If I want it to do classification it
expects a "factor" for y, but I am at a loss for the easiest way to
call convert a
Hate to keep replying to my own message but...
I thought I'd throw a newer version of R at this problem. My above errors
are with 2.7.1 and I thought I'd test with 2.8.2 (my development box, where
all works well is at 2.7.2). I kept my main 2.7.1 install in /usr/lib64 and
installed 2.8.2 into /u
With rpy2 (although there is currently no formal class for factors):
import rpy2.robjects as ro
vec = ro.StrVector(("a", "b", "a", "b"))
vec = ro.r["factor"](vec)
On Thu, 2009-04-09 at 19:38 -0400, David Warde-Farley wrote:
> Hi all,
>
> I'm somewhat new to Rpy, and trying to use the R r
There is even more in the fine manual:
http://rpy.sourceforge.net/rpy2/doc/html/introduction.html#linear-models
http://rpy.sourceforge.net/rpy2/doc/html/robjects.html#formulae
On Thu, 2009-04-09 at 21:10 +, Juls Night wrote:
> Many thanks!
>
> I see now how this works.
>
> Best,
> Juls
>
On Thu, 2009-04-09 at 15:59 -0400, Mark Larsen wrote:
> I have an R function that returns a list of Matrices and Vectors.
>
> I've been processing the return list like:
>
> rpyRV = rpy2.robjects.r.someFunc()
> for property,rObj in zip([i for i in rpyRV.getnames()],[i for i in
> rpyRV]):
> # d
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