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examples.development [2010/03/25 11:15]
mjnueda
examples.development [2010/05/05 10:39] (current)
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.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.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:
-{{:hypo_3go_masigfun.pdf?400|}}+\\ 
 +{{: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.
 +
examples.development.1269512110.txt.gz · Last modified: 2010/03/25 11:15 by mjnueda
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