> I have one more point I would like to add.
>
> When I run all of the code in R, it works just fine. If I make a small
> python file with exactly the code I ran in R, it gives me the 'not all
> arguments have the same length' error. I will continue to check my code, but
> I am suspicious that its having trouble with the surv_time variable and that
> the interface is really excepting surv.time and there is some
> mistranslation. I will also try using RPy2 to see if anything helps.
>
> Any further advice would be appreciated, but thanks for the help so far : )
>
> On Fri, Apr 15, 2011 at 9:06 AM, Peter <rpy-l...@maubp.freeserve.co.uk>wrote:
>
>> On Fri, Apr 15, 2011 at 4:56 PM, Anamaria Crisan <a...@genomedx.com>
>> wrote:
>> > I am using just Rpy. Would RPy2 be the solution?
>> >
>>
>> Possibly - and in the long term it would be worth looking at,
>> but there are quite a few API changes to beware of.
>>
>> Back in rpy (v1), to run an R command like:
>>
>> cindex(x=prob, surv.time=survTIME, surv.even=survEVENT)
>>
>> you should (as I recall) switch the dots to underscores in Python
>> for argument names etc:
>>
>> cindex(x=prob, surv_time=survTIME, surv_even=survEVENT)
>>
>> This is because dots are used in Python to access the methods
>> and attributes of an object. Argument names can't have dots,
>> that is what the SyntaxError is trying to tell you.
>>
>> The fact you then get an "not all arguments have the same length"
>> suggests there is a secondary problem in your script. I'm not
>> familiar with the R package survcomp so I can't really guess.
>>
>> Peter
>>
>
>
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