ORIOGEN (O rder R estricted I nference for O rdered G ene E xpressioN )



Advanced Inputs Screen:

Perform reclassification check

P-value for reclassification of profiles


Perform Reclassification Check:

Once a gene is declared significant by ORIOGEN, it is initially assigned to the profile with the largest goodness-of-fit statistic. However, in some situations the cluster assignment may require further refinements. For instance, consider the following two profiles:

 

In Figure 1 the mean expression of a gene (denoted by blue dots) increases from the first to the second time point and stays up at time point 3. Whereas in Figure 2 the mean expression increases from time point 1 to time point 2 and then it decreases at time point 3. In theory, both describe an umbrella shape. This is because the alternative hypothesis does not have strict inequalities between the population means, it allows "=". Figure 2 has a strict inequality between the means, while the profile in Figure 1 allows for equality between the means of the second and the third time points. Thus profile in Figure 1 can also be viewed as an increasing profile. In some applications, it may be important to distinguish between these two profiles. Similar re-classifications may be necessary for other profiles

You can completely disable the reclassification algorithm by choosing the "Skip the Reclassification" option. In this state, ORIOGEN will select profiles based solely on the goodness-of-fit statistic.

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P-value for reclassification:

This field specifies the level of significance to be used for re-classification purposes. The default level of significance for re-classification is set at 0.1. However, a user to can modify this choice by entering in this field the desired level of significance for re-classification. Note that, by lowering this level of significance you increase the possibility for a gene to have flat regions in its dose-response/time-course profile.

The above re-classification of profiles does not affect the gene selection process.

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