GRNmap Testing Report: Strain Run Comparisons 2015-05-27: Difference between revisions

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(→‎wt vs. dGLN3: Uploaded the files for dGLN3 vs. wt)
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==wt vs. dGLN3==
==wt vs. dGLN3==
*input.xlsx
*[[Media:Input 21 Gene Network Sigmoid Model Estimate WTvdGLN3 NW.xlsx| Input Sheet]]
*output.xlsx
*[[Media:Input 21 Gene Network Sigmoid Model Estimate WTvdGLN3 estimation output NW.xls| Output Sheet]]
*zipped figures
*[[Media:WT.dGLN3 figures NW.zip| Figures]]
*analysis.xlsx containing bar graphs
*analysis.xlsx containing bar graphs
*LSE:
*LSE: 30.0410
*Penalty term:
*Penalty term: N/A


==wt vs. dHMO1==
==wt vs. dHMO1==

Revision as of 11:16, 27 May 2015

Code Version: "current" version from Dr. Fitzpatrick 2014-09-18

MATLAB Version: 2014a

Computer on which the model was run: SEA120-03

  • Last two test categories (wt+dCIN5+dZAP1 and wt+dCIN5+dZAP1+dGLN3) cannot be run on SEA120-03 because the computer only has MATLAB 2014b. Error displayed when Fitzpatrick's code version is run:
Undefined function 'max' for input arguments of type 'matlab.graphics.GraphicsPlaceholder'.

Error in GRNmodel (line 15)
nfig        = max(figHandles);
  • For the first ten categories, we will upload data obtained from September 2014. To see if we can run the last two categories on 2014b without any glaring differences, we will first test wt alone on both 2014a (with Fitzpatrick's fall version of the code) and 2014b (with the code from the class BIOL398-04/S15). If the differences in estimated parameters are negligible, we could move on to run the last two categories (wt+dCIN5+dZAP1 and wt+dCIN5+dZAP1+dGLN3).
    • New code version: from BIO398 (Note: file zipped with code was used to test wt)
    • MATLAB version: 2014b
    • Computer on which the model was run: SEA201-03
      • Note: for these older versions of the code, the input file must be in the same folder as the code itself.


To get the LSE & the penalty term, type the following: 

Code for LSE:
GRNstruct.GRNOutput.lse_out

Code for Penalty
GRNstruct.GRNOutput.reg_out

wt alone

dCIN5 alone

dGLN3 alone

dHMO1 alone

dZAP1 alone

All Strains

wt vs. dCIN5

wt vs. dGLN3

wt vs. dHMO1

  • input.xlsx
  • output.xlsx
  • zipped figures
  • analysis.xlsx containing bar graphs
  • LSE:
  • Penalty term:

wt vs. dZAP1

  • input.xlsx
  • output.xlsx
  • zipped figures
  • analysis.xlsx containing bar graphs
  • LSE:
  • Penalty term:

wt + dCIN5 + dZAP1

  • input.xlsx
  • output.xlsx
  • zipped figures
  • analysis.xlsx containing bar graphs
  • LSE:
  • Penalty term:

wt + dCIN5 + dZAP1 + dGLN3

  • input.xlsx
  • output.xlsx
  • zipped figures
  • analysis.xlsx containing bar graphs
  • LSE:
  • Penalty term:

Results and Discussion

  • What other questions should be answered to help us further analyze the data?
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