Sequence Odds Ratio

The formula for the sequence odds ratio is:

Seqs A / Total Sequences in A
Seqs B / Total Sequences in B

The results of the DGED are ordered by the odds ratio, with all cases of "NaN" coming at the head of the list. "NaN" stands for "not a number" and occurs when the denominator of the equation is 0, i.e., there are no sequences of a gene in pool B.

Significance Test

To measure the significance of differences in transcript expression, we follow the method described in

A public database for gene expression in human cancers. Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak K, Papadopoulos N, Vogelstein B, Kinzler KW, Strausberg RL, Riggins GJ. Cancer Res. 1999 Nov 1;59(21):5403-7.

Briefly, the method uses Bayesian analysis to compute the probability that sampling error accounts for the fact that a tag has been observed to occur more frequently in one library pool than in a second library pool. The method uses an assumed prior distribution of tag frequency and the observed frequencies to compute the posterior probability, P, that the underlying frequency of a tag in one collection of tissues exceeds, by some factor F, the underlying frequency of the tag in a second collection of tissues. The value of P ranges from 0% (very likely that the results are not due to sampling error) to 100% (very likely that the results are due to sampling error).

Examples of combinations of F and P:

F	P	Results
3	.20	Moderate probability that the tag occurs three times as frequently in one pool as in the other
3	.01	Strong probability that the tag occurs three times as frequently in one pool as in the other
1	.20	Moderate probability that the tag occurs more frequently (even only slightly more frequently) in one pool than in the other
1	.01	Strong probability that the tag occurs more frequently (even only slightly more frequently) in one pool than in the other