GRNmap Testing Report .xlsx vs. .xls 2015-05-27: Difference between revisions

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==GRNmap Testing Report==
==Test Conditions==
*Date started: 2015-05-27
*Date started: 2015-05-27
*Code Version: "current" version from Dr. Fitzpatrick 2014-09-18
*Test Performed by: [[User:Tessa A. Morris| Tessa A. Morris]], [[Tessa A. Morris Electronic Lab Notebook| Electronic Notebook]]
*[https://github.com/kdahlquist/GRNmap/archive/v1.0.6.zip GRNmap] version 1.0.6
*Code Version: [https://github.com/kdahlquist/GRNmap/archive/v1.0.6.zip GRNmap] version 1.0.6
*MATLAB Version: 2014b
*MATLAB Version: 2014b
*Model was run on the following computer: Row#2 4
*Computer on which the model was run: Row 2 4th from door


==Input, Output, and Plots==
==Purpose==
*The purpose was to test if there was a difference between running an .xlsx and an .xls file.
*[https://github.com/kdahlquist/GRNmap/issues/97 Issue 97]
==Results==
*22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xls
*22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xls
**[[Media:22-genes 47-edges Dahlquist-data MM estimation fixP-1 graph.xls| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xls]]
**[[Media:22-genes 47-edges Dahlquist-data MM estimation fixP-1 graph.xls| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xls]]
**[[Media:22-genes 47-edges Dahlquist-data MM estimation fixP-1 graph output.xls| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph_output.xls]]
**[[Media:22-genes 47-edges Dahlquist-data MM estimation fixP-1 graph output.xls| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph_output.xls]]
**[[Media:22-genes 47-edges Dahlquist-data MM estimation fixP-1 graph plots.zip| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph_plots.zip]]
**[[Media:22-genes 47-edges Dahlquist-data MM estimation fixP-1 graph plots.zip| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph_plots_xls.zip]]
*22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xlsx
*22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xlsx
**[[Media:22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph]]
**[[Media:22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xlsx]]
**[[Media:22-genes 47-edges Dahlquist-data MM estimation fixP-1 graph output.xlsx| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph_output.xlsx]]
**[[Media:22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph_plots_xlsx.zip]]
*22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xls
*22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xls
**[[Media:22-genes 47-edges Dahlquist-data Sigmoid estimation fixb-1 fixP-1 graph.xls| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xls]]
**[[Media:22-genes 47-edges Dahlquist-data Sigmoid estimation fixb-1 fixP-1 graph.xls| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xls]]
**[[Media:22-genes 47-edges Dahlquist-data Sigmoid estimation fixb-1 fixP-1 graph output.xls| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph_output.xls]]
**[[Media:22-genes 47-edges Dahlquist-data Sigmoid estimation fixb-1 fixP-1 graph xls.zip| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph_xls.zip]]
*22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xlsx
*22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xlsx
**[[Media:22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xlsx]]
**[[Media:22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xlsx]]
**[[Media: 22-genes 47-edges Dahlquist-data Sigmoid estimation fixb-1 fixP-1 graph output.xlsx| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph_output.xlsx]]
**[[Media: 22-genes 47-edges Dahlquist-data Sigmoid estimation fixb-1 fixP-1 graph xlsx.zip| 2-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph_xlsx.zip]]


==Methods==
==Discussion==
=== Preparing the input sheets ===
*If a file is in the .xls format, the output will also be .xls. GRNsight can only handle .xlsx files so the file will need to be converted into a .xlsx before being visualized using GRNsight.  
# Download [[Media:22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph]] and [[Media:22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph.xlsx| 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph]] from a previous experiment [[GRNmap Test Inputs| comparing the sixteen possible options for the input sheet]].  
*The [[Media:GRNmap Testing Report xlsx vs xls 2015-05-27 Summary Statistics.xlsx| Summary Statistics]] showed that there was not a notable difference between using .xlsx and .xls.  
# Both of these files should be in .xlsx format. Open them in Microsoft Excel, enable editting and save as an .xls file.  
*The maximum of the MM difference matrix was 4.74681E-07 and the maximum of the Sigmoidal difference matrix was 4.51574E-06.  
# Upload the input sheets to openwetware.  
*The small differences were due to rounding errors, rather than an error in the program.  
===Running GRNmap===
# Download the current version of [https://github.com/kdahlquist/GRNmap/archive/v1.0.6.zip GRNmap] from GitHub, in this case we are using version 1.0.6. 
#* Save it into a new folder called "GRNmap" on the Desktop.
#* Unzip the file by right-clicking on it and choosing 7-zip > Extract here.
# Drag the four input sheets into the "matlab" subfolder of "GRNmap-1.0.6". To keep it organized I created two folders within the "matlab" subfloder called "Need to Run" and "Ran".
# Open the "GRNmap-1.0.6" folder and open the "matlab" subfolder.  Double-click on the file "GRNmodel.m" to open GRNmap in MATLAB 2014b.
# Click on the green triangle "Run" button to run the model.
#* You will be prompted by an Open dialog to find your input file that you created in the previous section. Browse and select this input file and click OK.
#* Note that the Open dialog will default to show files of <code>*.xlsx</code> only.  If your file is saved as <code>*.xls</code>, you will need to select the drop-down menu to show all files.
#* A window called "Figure 1" will appear.  The counter is showing the number of iterations of the least squares optimization algorithm. The top plot is showing the values of all the parameters being estimated. You should see some movement of the diamonds each time the counter iterates.
# Once the model has completed its run, plots showing the expression over time for all of the genes in the network will appear if "makeGraphs" was set to 1. The plots will automatically be saved as <code>*.jpg</code> files in the same folder as your input file.  Compile the figures into a folder following the naming convention described earlier. Compress this folder by right clicking then selecting "7-zip" and "Add to archive...". Make sure the archive format is "zip."
# Upload the output sheet and the zipped folder with the output plots onto openwetware.
# After the initial run, type the commands "clear all" and "close all" then "GRNmodel" and select the input sheet to run.


==Observations==
[[Category:Dahlquist Lab]]
*If a file is in the .xls format, the output will also be .xls. GRNsight can only handle .xlsx files so the file will need to be converted into a .xlsx before being visualized using GRNsight.
[[Category: GRNmap]]
{{Template:Tessa A. Morris ELN}}

Latest revision as of 10:15, 3 June 2015

Test Conditions

Purpose

  • The purpose was to test if there was a difference between running an .xlsx and an .xls file.
  • Issue 97

Results

Discussion

  • If a file is in the .xls format, the output will also be .xls. GRNsight can only handle .xlsx files so the file will need to be converted into a .xlsx before being visualized using GRNsight.
  • The Summary Statistics showed that there was not a notable difference between using .xlsx and .xls.
  • The maximum of the MM difference matrix was 4.74681E-07 and the maximum of the Sigmoidal difference matrix was 4.51574E-06.
  • The small differences were due to rounding errors, rather than an error in the program.
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