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examples.development [2010/03/25 11:16] mjnueda |
examples.development [2010/05/05 10:39] mjnueda |
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====== Development Example====== | ====== Development Example====== | ||

- | | + | Data:{{:subset_development_4t_data.zip|}} |

- | Data:{{:subset_hypoxia_4t_data.zip|}} | + | |

\\ | \\ | ||

Covariates:{{:development_covariates.txt|}} | Covariates:{{:development_covariates.txt|}} | ||

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Variability associated to each factor: | Variability associated to each factor: | ||

* Time 25.86 % | * Time 25.86 % | ||

- | * Treatment+TimexTreatment 37.56 % | + | * Treatment+TimexTreatment 37.52 % |

* Residuals 36.62 % | * Residuals 36.62 % | ||

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====== ASCA-Functional ====== | ====== ASCA-Functional ====== | ||

+ | \\ | ||

+ | By applying ASCA-Functional to the first component of the submodel Treatment+TimexTreatment and considering a significant level of 0.05 in the GSA analysis we detected as significant 13 functional categories. | ||

+ | The categories with an adjusted p-value less than 0.05 appear in the first two tables of the ASCA-Functional results. | ||

+ | \\ | ||

+ | {{:hypoxia_ascafunt.png?600|}} | ||

+ | |||

====== maSigPro ====== | ====== maSigPro ====== | ||

- | General trends showed with ASCA-genes module suggest that a quadratic model can be adequate to study gene expression evolution. By applying maSigPro with degree=2 (the quadratic model), R-squared=0.7 and alpha=0.05 we obtained as significant: | + | General trends showed with ASCA-genes module suggest that a quadratic model can be adequate to study gene expression evolution. By applying maSigPro with degree=2 (the quadratic model), R-squared=0.8 and alpha=0.05 we obtained as significant: |

* 1307 genes with changes in the trajectory of A. | * 1307 genes with changes in the trajectory of A. | ||

* 1158 genes with differences between the trajectories of the groups B and A. | * 1158 genes with differences between the trajectories of the groups B and A. | ||

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The trajectory plots of these categories are the following: | The trajectory plots of these categories are the following: | ||

+ | \\ | ||

+ | {{:hypoxia_3go_masigfun.png?600|}} | ||

====== PCA-maSigFun ====== | ====== PCA-maSigFun ====== | ||

+ | Finally we run PCA-maSigFun with degree=2, R-squared=0.8 and alpha=0.05. This tool selected as statistically significant the following number of categories for the experimental groups: | ||

+ | * 1466 categories with changes in the trajectory of A. | ||

+ | * 1100 categories with differences between the trajectories of the groups B and A. | ||

+ | * 1469 categories with differences between the trajectories of the groups C and A. | ||

+ |