GRNmap Testing Report Identical Runs with Same Code Version and Same Input Workbook 2015-06-01: Difference between revisions

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== Results ==
== Results ==
* Input sheet: [[Media:]]
* Output sheet: [[Media:]]
* Output .mat file (zipped): [[Media:]]
** LSE:
** Penalty term:
** Number of iterations (counter):
* Figures (all expression graphs .jpg files zipped together): [[Media:]]
* Save the progress figure containing the counts manually: [[Media:]]
* analysis.xlsx containing bar graphs: [[Media:]]
* GRNsight figure of unweighted network: [[Image:]]
* GRNsight figure of weighted network: [[Image:]]
*4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-1
*4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-1
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-1.xlsx]]
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-1.xlsx]]
Line 33: Line 20:
** Number of iterations: 12900
** Number of iterations: 12900
*4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2
*4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2.xlsx]]
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2_output.xlsx]]
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2_output.mat]]
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2
**[[Media:4-genes_6-edges_artificial-data_Sigmoidal_estimation_fixb-0_fixP-0_graph_copy-2_plots.zip]]
** LSE: 3.5295e-08
** LSE: 3.5295e-08
** Penalty term: 13.6109
** Penalty term: 13.6109
** Number of iterations: 12900
** Number of iterations: 12900
*4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-1
**[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-1.xlsx]]
**[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-1_output.xlsx]]
**[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-1_output.mat]]
**[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-1_plots.zip]]
**LSE: 0.1077
**Penalty term: 63.1164
**Number of iterations: 8700
*4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-2
**[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-2.xlsx]]
**[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-2_output.xlsx]]
**[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-2_output.mat]]
**[[Media:4-genes_6-edges_artificial-data_MM_estimation_fixP-0_graph_copy-2_plots.zip]]
**LSE: 0.1077
**Penalty term: 63.1164
**Number of iterations: 8700
*[[Media:GRNmap Testing Report Identical Runs with Same Code Version and Same Input Workbook analysis 2015-06-02.xlsx| Analysis Workbook]]


== Discussion ==
== Discussion ==
* Discuss the results of the test with regards to the stated purpose. Additionally, answer the relevant questions below:
*The LSE, Penalty term, and the counter are the same between the two copies.  
** Examine the graphs that were output by each of the runs. Which genes in the model have the closest fit between the model data and actual data? Which genes have the worst fit between the model and actual data? Why do you think that is? (Hint: how many inputs do these genes have?) How does this help you to interpret the microarray data?
*The difference between the network_optimized_weights, optimized_production_rates, and optimized_threshold_b  values of two copies of the Sigmoidal_estimation_fixb-0_fixP-0_graph was zero.  
** Which genes showed the largest dynamics over the timecourse? In other words, which genes had a log fold change that is different than zero at one or more timepoints. The p values from the Week 11 ANOVA analysis are informative here. Does this seem to have an effect on the goodness of fit (see question above)?
*The difference between the network_optimized_weights and optimized_production_rates values of two copies of the MM_estimation_fixP-0_graph was zero (no sheet for optimized_threshold_b).
** Which genes showed differences in dynamics between the wild type and the other strain your group is using? Does the model adequately capture these differences? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?
** Examine the bar charts comparing the weights and production rates between the two runs. Were there any major differences between the two runs? Why do you think that was? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?
** What other questions should be answered to help us further analyze the data?
[[Category:GRNmap]]
[[Category:GRNmap]]
[[Category:Dahlquist Lab]]
[[Category:Dahlquist Lab]]

Latest revision as of 16:19, 2 June 2015

Test Conditions

  • Date: 2015-06-02
  • Test Performed by: Tessa A. Morris, Electronic Notebook
  • Code Version: Current version of GRNmap-beta as of 2:30 pm 2015-06-02
  • MATLAB Version: 2014b
  • Computer on which the model was run: Row 2 4th from door

Purpose

  • The purpose of this test was to compare successive identical runs with same version code and same input workbook to make sure that they are the same.
  • Issue 99

Results

Discussion

  • The LSE, Penalty term, and the counter are the same between the two copies.
  • The difference between the network_optimized_weights, optimized_production_rates, and optimized_threshold_b values of two copies of the Sigmoidal_estimation_fixb-0_fixP-0_graph was zero.
  • The difference between the network_optimized_weights and optimized_production_rates values of two copies of the MM_estimation_fixP-0_graph was zero (no sheet for optimized_threshold_b).
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