We successfully completed a one-day training course for ~40 people on how to use anthill, and everyone is now an expert, right?

The latest version of the anthill training notes are now available at this link: AnthillTrainingNotes

We successfully completed a one-day training course for ~40 people on how to use anthill, and everyone is now an expert, right?

The latest version of the anthill training notes are now available at this link: AnthillTrainingNotes

Here we are testing the ROV in a pool.

There are two Perl repositories available on CPAN that deal with Chi-squared analysis(`Statistics::ChiSquare`

and `Statistics::Distributions)`

. However neither one outputs the Chi-squared value for the analysis of two binary populations.

We can use the formula below to calculate the Chi-squared value with one degree of freedom.

χ2 = [n(ad – bc)2] / [(a + b) (c + d) (a + c) (b + d)]

n = a + b + c + d

Where:

variable | population 1 | population 2 |
---|---|---|

+ | a | b |

– | c | d |

Example:

Suppose we wish to determine the relationship between disease in two species. Both disease and the species are binary variables, so the Chi-squared test is applied:

Diseased | species 1 | species 2 |
---|---|---|

No | 57 | 36 |

Yes | 63 | 88 |

n = (57 + 36 + 63 + 88) = 244

χ^{2} = [244*(57*88 – 36*63)^{2}] / [(57 + 36) (63 + 88) (57 + 63) (36 + 88)]

χ^{2} = 8.81

The critical Chi-squared distribution P-values at 1 degree of freedom are:

D.F. | 0.1 | 0.05 | 0.025 | 0.01 | 0.005 |
---|---|---|---|---|---|

1 | 2.71 | 3.84 | 5.02 | 6.63 | 7.88 |

The χ^{2} value (8.82) is below the P-value 0.005.

Since the corresponding P-value is less than 0.05 (P<0.05), the data suggest that the prevalence of disease is significantly higher in species 2. Therefore we reject the null hypothesis.

Below is a Perl subroutine to automatically calculate Chi-squared.

```
sub chi_squared {
my ($a,$b,$c,$d) = @_;
return 0 if($b+$d == 0);
my $n= $a + $b + $c + $d;
return (($n*($a*$d - $b*$c)**2) / (($a + $b)*($c + $d)*($a + $c)*($b + $d)));
}
print &chi_squared(57,36,63,88);
```

Output:

`8.81780430153469`

content

content:

tools and data content

Rob Edwards’ bioinformatics lab at San Diego State University is all about decoding life’s best kept secrets. These secrets are encoded, as you must have already guessed, in genomes of bacteria, archaea, eukaryotes and the viruses that infect them.

We use all kinds of computers, from clusters to cell phones, to solve the most unsolvable computational problems that help us better understand biology.

We are funded by the National Science Foundation to explore phage genomes, through our PhAnToMe project, and to explore phage metagenomes (and the unknown genes in them) through our new Viral Dark Matter Project.

Rob has collaborations all over the world, and has taught in Europe, Asia, and Latin America. We are currently funded by the Department of Education through the Fund for the Improvement of Postsecondary Education and the Brazilian Ministry of Education (FIPSE-CAPES) to develop a marine sciences course in Brazil.

Rob has published over 60 peer-reviewed papers, and given an equal number of talks. A short biography about Rob describes his background, and his CV has more information. You can contact Rob for more information.

In here, we will soon have a great description of our research.

**PhAnToMe**

Here is a list of interesting questions that we are working on, and advice to graduate students interested in working in the lab.