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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Theoretical questions >> Sequence Analysis >> Odd GARD output http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1311881542 Message started by CrystalH on Jul 28^th, 2011 at 12:32pm

Title: Odd GARD output
Post by CrystalH on Jul 28^th, 2011 at 12:32pm

Hello,
I recently ran GARD and was wondering if this output is normal when no potential breakpoints are found, or if the "nan" is an error:

Breakpoint | LHS Raw p | LHS adjusted p | RHS Raw p | RHS adjusted p

At p = nan there are nan significant breakpoints
At p = nan there are nan significant breakpoints
At p = nan there are nan significant breakpoints

Mean splits identify: nan

Thank you.
-Crystal

Title: Re: Odd GARD output
Post by Art Poon on Dec 12^th, 2011 at 3:20pm

Hi Crystal,

Sorry for the delay in replying to this.
On perusing the GARDProcessor.bf, it seems to me that you might get a divide by zero error that would be manifested as "NaN" values if readPCount takes a value of 1. In the console output that reads "Loaded X partitions", what is X?

Cheers,
- art