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differential_expression_example [2010/09/30 17:18]
mbleda
differential_expression_example [2010/09/30 17:44] (current)
mbleda
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       - Set also **Benjamini and Hochberg (BH), FDR** as the multiple-test correction.       - Set also **Benjamini and Hochberg (BH), FDR** as the multiple-test correction.
       - Set the adjusted p-value in **0.05**(([[adjustedpvalues|Adjusted p-value]])).       - Set the adjusted p-value in **0.05**(([[adjustedpvalues|Adjusted p-value]])).
-      - **Submit** and when the job has finished, take a look at the results. \\ \\ {{ :​images:​differential_expression_example:​heatmap.png |Heatmap}} \\ \\ What you can see after the analysis is a **heatmap** with the intensities for these genes that are significantly differentially expressed. Each <fc #​008000>​**gene**</​fc>​ is represented in a row and each <fc #​808000>​**condition or array**</​fc>​ is represented in a column. High intensity measurements of gene expression are represented in <fc #​FF0000>​**red**</​fc>​ colors while <fc #​0000FF>​**blue**</​fc>​ colors represent lower measurements. Genes are sorted according to their expression patterns in the same order as they are in the output file. Experimental conditions or arrays are ordered depending on their labels. \\ \\  {{ :​images:​differential_expression_example:​de_files.png |Files to dowload}} \\ \\ The red square in the image above this words shows the number of genes differentially expressed in a significant way. In green, all the files you can download just clicking: \\ \\ - <fc #​008000>​**1.**</​fc>​ //__Limma output file__//: this file contains a table with the statistic value, p-value, and adjusted p-value for each one of the genes in the array. \\ - <fc #​008000>​**2.**</​fc>​ //​__Significative values dataset__//:​ An **expression data matrix**(([[babelomics_expression_data|Expression Data Matrix]])) only containing ​those genes differentially expressed. \\ - <fc #​008000>​**3.**</​fc>​ //​__Significative values table__//: As well as in 'limma output'​ (1), it is a file contains a table with the statistic value, p-value, and adjusted p-value but just for those genes which are differentially expressed. \\ \\ At the bottom of the page you will see a collection of links which will help you go on with the **Functional profiling analysis**((To continue with this analysis, click [[fatigo_pipeline_example|here]].)). \\ \\ {{ :​images:​differential_expression_example:​continue_processing.png |Continue processing}}+      - **Submit** and when the job has finished, take a look at the results. \\ \\ {{ :​images:​differential_expression_example:​heatmap.png |Heatmap}} \\ \\ What you can see after the analysis is a **heatmap** with the intensities for these genes that are significantly differentially expressed. Each <fc #​008000>​**gene**</​fc>​ is represented in a row and each <fc #​808000>​**condition or array**</​fc>​ is represented in a column. High intensity measurements of gene expression are represented in <fc #​FF0000>​**red**</​fc>​ colors while <fc #​0000FF>​**blue**</​fc>​ colors represent lower measurements. Genes are sorted according to their expression patterns in the same order as they are in the output file. Experimental conditions or arrays are ordered depending on their labels. \\ \\  {{ :​images:​differential_expression_example:​de_files.png |Files to dowload}} \\ \\ The red square in the image above this words shows the number of genes differentially expressed in a significant way. In green, all the files you can download just clicking: \\ \\ - <fc #​008000>​**1.**</​fc>​ //__Limma output file__//: this file contains a table with the statistic value, p-value, and adjusted p-value for each one of the genes in the array. \\ - <fc #​008000>​**2.**</​fc>​ //​__Significative values dataset__//:​ An **expression data matrix**(([[babelomics_expression_data|Expression Data Matrix]])) only containing ​the most significant 500 genes differentially expressed. \\ - <fc #​008000>​**3.**</​fc>​ //​__Significative values table__//: As well as in 'limma output'​ (1), it is a file contains a table with the statistic value, p-value, and adjusted p-value but just for the most significant 500 genes which are differentially expressed. \\ \\ At the bottom of the page you will see a collection of links which will help you go on with the **Functional profiling analysis**((To continue with this analysis, click [[fatigo_pipeline_example|here]].)). \\ \\ {{ :​images:​differential_expression_example:​continue_processing.png |Continue processing}}
  
  
  
  
differential_expression_example.txt ยท Last modified: 2010/09/30 17:44 by mbleda
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