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

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*Computer on which the model was run: Row 2 4th from door
*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]]

Revision as of 17:15, 2 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

Methods

Preparing the input sheets

  1. Download 22-genes_47-edges_Dahlquist-data_MM_estimation_fixP-1_graph and 22-genes_47-edges_Dahlquist-data_Sigmoid_estimation_fixb-1_fixP-1_graph from a previous experiment comparing the sixteen possible options for the input sheet.
  2. Both of these files should be in .xlsx format. Open them in Microsoft Excel, enable editting and save as an .xls file.
  3. Upload the input sheets to openwetware.

Running GRNmap

  1. Download the current version of 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.
  2. 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".
  3. 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.
  4. 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 *.xlsx only. If your file is saved as *.xls, 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.
  5. 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 *.jpg 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."
    • Note that because in this case the file names are essentially the same with the file extension being different, there may be some issues. I added _xls or _xlsx to the names of the folders so they would not overwrite. I did not run into any issue with Matlab because I moved the .mat files into the folder "Ran" for the first run (.xls) but when I tried to move the second output (.xlsx) there was an issue because it had the exact same name. To rectify this, windows added a (2) to the end of the second .mat file). The .mat files will likely not be needed in this experiment, so it should not cause problems.
  6. Upload the output sheet and the zipped folder with the output plots onto openwetware.
  7. After the initial run, type the commands "clear all" and "close all" then "GRNmodel" and select the input sheet to run.

Analyzing the Results

  1. The production rate and threshold b values will not be used in the data analysis. The version of Matlab has the previously documented errors with P and b for the Sigmoidal. The Michealis Menten model does not make use of the term b and also has an error with the production rate.
  2. The simplest way to understand if there is a difference in the weights between .xlsx and .xls is to subtract the matrices. This is done in excel by selecting a blank area with the same dimensions as the two matrices. In the formula bar type =(All of Matrix "xls")-(All of Matrix "xlsx") then press "Control" "Shift" "Enter". These should all be pressed at the same time.
  3. Find and report the maximum of the difference matrices. This is done by typing =MAX(Difference Matrix) in a new cell.

Observations

  • 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.

Dahlquist Lab Navigation

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