Error integer overflow

[IamIamI]

Hi,

I have been using the Rqtl package for a couple of months now and i really like it. I have done several experiments on small datasets and got great resuls out of it. Last week however, i got a dataset that contained 103.943 markers and got the following error during the first est.rf() step.

Error in rep(0, n.mar * n.mar) : invalid 'times' argument
In addition: Warning message:
In n.mar * n.mar : NAs produced by integer overflow

My guestimation is that my datasets too large seeing as the n.mar * n.mar (103.943^2) is too large for 32bit integers. But i'm unsure how to solve this, do i have to install an external package that allows me to store 64bit integers or is this is a fixed limitation of the Rqtl package?

Greetings,
Lesley

[Karl Broman]

You won't be able to use est.rf() with so many markers, because it seeks to calculate the linkage for *all* pairs of markers, and that's just too time-consuming and uses too much memory, even with a 64bit system.

There's no strict limit on the number of markers, but there are a number of functions that won't work well with very large data sets.

karl

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