User contributions for Katrina Sherbina

13 August 2014

• 22:0722:07, 13 August 2014 diff hist +1 m Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Comparing Significant Changes in Expression Between Two Strains: Added missing period
• 22:0722:07, 13 August 2014 diff hist +245 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Comparing Significant Changes in Expression Between Two Strains: Added link to earlier section describing Benjamini & Hochberg Correction
• 22:0422:04, 13 August 2014 diff hist 0 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Calculate the F Statistic: Changed degrees of freedom T, N-T to q, n-p to match the section before describing the statistical test overall
• 22:0222:02, 13 August 2014 diff hist 0 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Analyzing Significant Gene Expression Changes Within Each Strain: Corrected references to some variables
• 21:5321:53, 13 August 2014 diff hist +354 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Comparing Significant Changes in Expression Between Two Strains: Elaborated on F statistic and p value calculation for two strain statistics
• 21:4821:48, 13 August 2014 diff hist −74 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Changed the if strcmpi(strain1,'wt') == 1 loop in the biggest for loop
• 21:4721:47, 13 August 2014 diff hist −9 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: removed break in code box
• 21:4621:46, 13 August 2014 diff hist +59 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Added a new variable indm to the biggest for loop to get rid of error occurring when code run line by line
• 21:4321:43, 13 August 2014 diff hist +102 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Created two new variables in the if strcmpi(strain1,'wt') == 0 loop to get rid of error in running code line by line
• 20:5520:55, 13 August 2014 diff hist +6 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Analyzing Significant Gene Expression Changes Within Each Strain: Changed total number of hypotheses from "n" to "m"
• 20:5320:53, 13 August 2014 diff hist 0 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Analyzing Significant Gene Expression Changes Within Each Strain: Corrected
• 20:4520:45, 13 August 2014 diff hist +6 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Added an "end" at the very end of the big for loop
• 20:4120:41, 13 August 2014 diff hist +129 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Analyzing Significant Gene Expression Changes Within Each Strain: Corrected description of degrees of freedom
• 20:3620:36, 13 August 2014 diff hist 0 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Analyzing Significant Gene Expression Changes Within Each Strain: Corrected F statistic equation
• 20:3620:36, 13 August 2014 diff hist +7 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Comparing Significant Changes in Expression Between Two Strains: Added a μ after each occurrence of average log fold change in first paragraph
• 20:3220:32, 13 August 2014 diff hist +366 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Comparing Significant Changes in Expression Between Two Strains: Added some equations in description of two strain comparison statistics
• 20:1220:12, 13 August 2014 diff hist +221 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Added to the NOTE about error in running code piece by piece
• 19:5619:56, 13 August 2014 diff hist +74 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Added comment within code block to describe the variable "Yh"
• 19:5319:53, 13 August 2014 diff hist +17 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Comparing Significant Changes in Expression Between Two Strains: Put in a switch before the if loop that creates the plots to control whether are not the plots are created
• 19:4719:47, 13 August 2014 diff hist −21 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Modified code to designate indices for each strain and time point as a result of modification to who the data is imported
• 19:0019:00, 13 August 2014 diff hist +11 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Modified the code that imports numerical and character data from input Excel workbook
• 18:5618:56, 13 August 2014 diff hist +464 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Added lines of code that allow the user to specify if they would like to see plots for the genes with a p value of less than 0.05
• 18:5118:51, 13 August 2014 diff hist +9 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Adjusted appearance of code so that it is within a box
• 18:4918:49, 13 August 2014 diff hist +190 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Modified the description of code that imports data that the user must edit
• 05:2305:23, 13 August 2014 diff hist 0 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Calculate the F Statistic: Made correction to description of formula B2-$Y2 in direction to double click the lower right hand corner

21 July 2014

• 23:3923:39, 21 July 2014 diff hist −13 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Better separated the part of the code corresponding to the warning
• 23:3823:38, 21 July 2014 diff hist +234 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Finding a General Linear Model in MATLAB: Documented an error when running the protocol piece by piece rather than all the way through
• 21:1021:10, 21 July 2014 diff hist +87 Dahlquist:Modified ANOVA and p value Corrections for Microarray Data →Calculating the F statistic and p value corrections in MATLAB: Gave a detailed description of how to specify the input variables filename, sheetname, and strain
• 20:1620:16, 21 July 2014 diff hist +173 Dahlquist:Microarray Data Processing in R →Create MA Plots and Box Plots for the GCAT Chips: Added the call browser() after to plot commands to allow the user to pause at the plot before continuing with the rest of the code
• 19:3319:33, 21 July 2014 diff hist 0 Dahlquist:Microarray Data Processing in R →Create MA Plots and Box Plots for the GCAT Chips: Changed an index in for loop that generates MA plots
• 19:3219:32, 21 July 2014 diff hist 0 Dahlquist:Microarray Data Processing in R →Create MA Plots and Box Plots for the GCAT Chips: Corrected index in for loop to calculate intensity values after averaging duplicate genes
• 19:3019:30, 21 July 2014 diff hist +1 Dahlquist:Microarray Data Processing in R →Create MA Plots and Box Plots for the GCAT Chips: Replaced a piece of hard coding
• 18:5718:57, 21 July 2014 diff hist +1 Dahlquist:Microarray Data Processing in R →Create MA Plots and Box Plots for the GCAT Chips: Indented a line to make it appear as a line of code
• 18:3918:39, 21 July 2014 diff hist 0 Dahlquist:Microarray Data Processing in R →Create MA Plots and Box Plots for the GCAT Chips: Changed rl to r1
• 18:3818:38, 21 July 2014 diff hist 0 Dahlquist:Microarray Data Processing in R →Create MA Plots and Box Plots for the GCAT Chips: Corrected variable name (lr to rl)
• 18:3618:36, 21 July 2014 diff hist +5 Dahlquist:Microarray Data Processing in R →Create MA Plots and Box Plots for the GCAT Chips: Corrected more variable names
• 18:3518:35, 21 July 2014 diff hist +5 Dahlquist:Microarray Data Processing in R →Create MA Plots and Box Plots for the GCAT Chips: Corrected the name of a variable
• 18:1518:15, 21 July 2014 diff hist +293 Dahlquist:Microarray Data Processing in R →Input Files for R: Added a description of the microarray chips normalized

15 July 2014

• 01:2401:24, 15 July 2014 diff hist +135 My Computational Journal Summer 2014 →July 14, 2014: Discussed next step current
• 00:4000:40, 15 July 2014 diff hist +316 My Computational Journal Summer 2014 →July 14, 2014: Wrote done some observations based on simulation
• 00:1800:18, 15 July 2014 diff hist +775 My Computational Journal Summer 2014 →July 14, 2014: Began writing about results of simulations with a fully connected, all positive weights 4-gene network
• 00:0800:08, 15 July 2014 diff hist +19 My Computational Journal Summer 2014 Added a new journal entry date

12 July 2014

• 04:3904:39, 12 July 2014 diff hist +1,199 My Computational Journal Summer 2014 →July 11, 2014: Discussed results for simulation run for a four gene fully connected network
• 04:3104:31, 12 July 2014 diff hist +1,031 My Computational Journal Summer 2014 →July 11, 2014: Described networks for which simulations were run and the results of these simulations for one of the networks
• 04:2304:23, 12 July 2014 diff hist +19 My Computational Journal Summer 2014 Added a new journal entry date

11 July 2014

• 05:0805:08, 11 July 2014 diff hist +1,958 My Computational Journal Summer 2014 →July 10, 2014: Discussed some patterns that I observed from plots of the model average and stats.
• 04:5704:57, 11 July 2014 diff hist +19 My Computational Journal Summer 2014 Added a new journal entry date

10 July 2014

• 00:3700:37, 10 July 2014 diff hist +268 My Computational Journal Summer 2014 →July 9, 2014: Ran multiple simulations experimenting with different parameter values
• 00:3600:36, 10 July 2014 diff hist +18 My Computational Journal Summer 2014 Added a new journal entry date

9 July 2014

• 21:0121:01, 9 July 2014 diff hist +483 My Computational Journal Summer 2014 →July 8, 2014: Wrapped up the entry with some observations