Re: [R] fisher.test FEXACT error 7

From: Ken Edwards <ke1_at_sanger.ac.uk>
Date: Mon 26 Jul 2004 - 20:11:29 EST

Thanks Sundar,

That changes the behaviour of R, but only in so far as it waits longer before giving the same error:

fisher.test(testDataTwoColumns, workspace = 2e8) Error in fisher.test(testDataTwoColumns, workspace = 2e+08) :

        FEXACT error 7.
LDSTP is too small for this problem.
Try increasing the size of the workspace.

...There also seems to be an upper limit of how big the workspace can be...

 > fisher.test(testDataTwoColumns, workspace = 2e9) Error in fisher.test(testDataTwoColumns, workspace = 2e+09) :

        negative length vectors are not allowed  > fisher.test(testDataTwoColumns, workspace = 2e10) Error in fisher.test(testDataTwoColumns, workspace = 2e+10) :

        NAs in foreign function call (arg 10) In addition: Warning message:
NAs introduced by coercion

A further question - do you (or anyone else) think that this is a problem with the physical capabilities of the box that I'm running on, or is it likely to be an upper limit with the amount of data that the algorithm can handle?

Many thanks,

Ken

Sundar Dorai-Raj wrote:

>
>
> Ken Edwards wrote:
>
>> Hello,
>> I have an error message that doesn't seem to make sense in that
>> having read the R documentation I was under the impression that R was
>> able to grab as much memory as it needed, and has been able to do so
>> for some time, so the advice given below about increasing the size of
>> the workspace is redundant.
>> If I'm right, does anyone have a solution to the problem of the size
>> of LDSTP? Or is this really a message about the limit of data size
>> that the function can handle?
>>
>> I have tried the function using test data containing a similar number
>> of (randomly generated) data points, and it worked then. There are
>> 258 data points in two columns (i.e. 2 * 134), if that helps.
>>
>> Any advice would be very much appreciated,
>>
>> Many thanks,
>>
>> Ken Edwards.
>>
>> R script below:
>>
>> fisher.test(testData)
>>
>> Error in fisher.test(testData) :
>> FEXACT error 7.
>> LDSTP is too small for this problem.
>> Try increasing the size of the workspace.
>>
>
> Maybe you should try increasing the workspace:
>
> fisher.test(testData, workspace = 2e6)
>
> --sundar
>
>
>



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