Dahlquist:Microarray Data Processing in R: Revision history

18 May 2015

• curprev 13:2213:22, 18 May 2015‎ Natalie Williams talk contribs‎ 35,014 bytes −4‎ deleted a double and after and in first bullet point

17 March 2015

• curprev 16:3416:34, 17 March 2015‎ Kam D. Dahlquist talk contribs‎ 35,018 bytes −6‎ →‎Within Array Normalization for the GCAT Chips: changed reference to Ontario to GCAT targets file
• curprev 16:3216:32, 17 March 2015‎ Kam D. Dahlquist talk contribs‎ 35,024 bytes +1‎ →‎Create a targets file with information about the .gpr files: fixed link to file
• curprev 16:3216:32, 17 March 2015‎ Kam D. Dahlquist talk contribs‎ 35,023 bytes +151‎ →‎Within Array Normalization for the Ontario Chips: added reference to new Ontario Targets file
• curprev 16:3116:31, 17 March 2015‎ Kam D. Dahlquist talk contribs‎ 34,872 bytes +1‎ →‎Within Array Normalization for the Ontario Chips: fixed format of link
• curprev 16:3016:30, 17 March 2015‎ Kam D. Dahlquist talk contribs‎ 34,871 bytes +150‎ →‎Within Array Normalization for the Ontario Chips: added reference to new Ontario targets file
• curprev 16:2916:29, 17 March 2015‎ Kam D. Dahlquist talk contribs‎ 34,721 bytes +362‎ →‎Create a targets file with information about the .gpr files: added link to new Ontario targets file

26 February 2015

• curprev 14:4214:42, 26 February 2015‎ Kam D. Dahlquist talk contribs‎ 34,359 bytes +260‎ note about 32- vs. 64-bit R giving slightly different results

18 August 2014

• curprev 13:4913:49, 18 August 2014‎ Kam D. Dahlquist talk contribs‎ 34,099 bytes +7‎ added zipped to limma download link
• curprev 13:4813:48, 18 August 2014‎ Kam D. Dahlquist talk contribs‎ 34,092 bytes +60‎ link to zipped limma package
• curprev 13:4113:41, 18 August 2014‎ Kam D. Dahlquist talk contribs‎ 34,032 bytes −186‎ updated link to R 3.1.0

13 August 2014

• curprev 09:5409:54, 13 August 2014‎ Kam D. Dahlquist talk contribs‎ 34,218 bytes +48‎ comment that need to fix links to R version and limma version

12 August 2014

• curprev 15:3315:33, 12 August 2014‎ Kam D. Dahlquist talk contribs‎ 34,170 bytes 0‎ changed some other instances of Wt to wt
• curprev 15:1115:11, 12 August 2014‎ Kam D. Dahlquist talk contribs‎ 34,170 bytes 0‎ →‎Create MA Plots and Box Plots for the Ontario Chips: changed "Wt" to "wt" in Ontario plots script to conform to changes made before in targets file.

23 July 2014

• curprev 13:5713:57, 23 July 2014‎ Kam D. Dahlquist talk contribs‎ 34,170 bytes +1,379‎ →‎Within Array Normalization for the GCAT Chips: added instructions and links for running scripts
• curprev 13:5113:51, 23 July 2014‎ Kam D. Dahlquist talk contribs‎ 32,791 bytes +654‎ →‎Within Array Normalization for the Ontario Chips: added links and instructions for running the script
• curprev 13:4113:41, 23 July 2014‎ Kam D. Dahlquist talk contribs‎ 32,137 bytes +92‎ →‎Within Array Normalization for the GCAT Chips: added link to GCAT targets file
• curprev 13:4113:41, 23 July 2014‎ Kam D. Dahlquist talk contribs‎ 32,045 bytes +90‎ →‎Data Normalization: added link to Ontario targest file
• curprev 13:4013:40, 23 July 2014‎ Kam D. Dahlquist talk contribs‎ m 31,955 bytes +7‎ →‎Create a targets file with information about the .gpr files: fixed link format
• curprev 13:3813:38, 23 July 2014‎ Kam D. Dahlquist talk contribs‎ 31,948 bytes +168‎ →‎Create a targets file with information about the .gpr files: link to Ontario and GCAT targets files added
• curprev 13:3313:33, 23 July 2014‎ Kam D. Dahlquist talk contribs‎ 31,780 bytes 0‎ →‎Input Files for R: fixed formatting of link

22 July 2014

• curprev 16:0416:04, 22 July 2014‎ Kam D. Dahlquist talk contribs‎ 31,780 bytes +199‎ →‎Create a targets file with information about the .gpr files: more explanation of top and bottom of GCAT chips
• curprev 16:0216:02, 22 July 2014‎ Kam D. Dahlquist talk contribs‎ 31,581 bytes +175‎ →‎Create a targets file with information about the .gpr files: made wt lowercase and noted downstream case sensitivity
• curprev 15:5915:59, 22 July 2014‎ Kam D. Dahlquist talk contribs‎ 31,406 bytes +203‎ →‎Input Files for R: added links to GCAT and Ontario microarray center
• curprev 15:5115:51, 22 July 2014‎ Kam D. Dahlquist talk contribs‎ 31,203 bytes −95‎ →‎Input Files for R: don't need to have separate folders for Ontario and GCAT so removed that instruction

21 July 2014

• curprev 13:1613:16, 21 July 2014‎ Katrina Sherbina talk contribs‎ 31,298 bytes +173‎ →‎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
• curprev 12:3312:33, 21 July 2014‎ Katrina Sherbina talk contribs‎ 31,125 bytes 0‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Changed an index in for loop that generates MA plots
• curprev 12:3212:32, 21 July 2014‎ Katrina Sherbina talk contribs‎ 31,125 bytes 0‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Corrected index in for loop to calculate intensity values after averaging duplicate genes
• curprev 12:3012:30, 21 July 2014‎ Katrina Sherbina talk contribs‎ 31,125 bytes +1‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Replaced a piece of hard coding
• curprev 12:1312:13, 21 July 2014‎ Kam D. Dahlquist talk contribs‎ 31,124 bytes +19‎ →‎Visualize the Normalized Data: warnings are OK
• curprev 12:0412:04, 21 July 2014‎ Kam D. Dahlquist talk contribs‎ 31,105 bytes +127‎ →‎Create MA Plots and Box Plots for the Ontario Chips: warning messages are ok
• curprev 12:0212:02, 21 July 2014‎ Kam D. Dahlquist talk contribs‎ 30,978 bytes +44‎ →‎Create MA Plots and Box Plots for the Ontario Chips: warning message OK
• curprev 11:5711:57, 21 July 2014‎ Katrina Sherbina talk contribs‎ 30,934 bytes +1‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Indented a line to make it appear as a line of code
• curprev 11:5311:53, 21 July 2014‎ Kam D. Dahlquist talk contribs‎ 30,933 bytes +144‎ →‎Create MA Plots and Box Plots for the GCAT Chips: warning message OK
• curprev 11:5011:50, 21 July 2014‎ Kam D. Dahlquist talk contribs‎ 30,789 bytes 0‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Changed a number to a bullet
• curprev 11:4911:49, 21 July 2014‎ Kam D. Dahlquist talk contribs‎ 30,789 bytes 0‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Corrected the line of code that averages duplicate spots on the GCAT chips
• curprev 11:3911:39, 21 July 2014‎ Katrina Sherbina talk contribs‎ 30,789 bytes 0‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Changed rl to r1
• curprev 11:3811:38, 21 July 2014‎ Katrina Sherbina talk contribs‎ 30,789 bytes 0‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Corrected variable name (lr to rl)
• curprev 11:3611:36, 21 July 2014‎ Katrina Sherbina talk contribs‎ 30,789 bytes +5‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Corrected more variable names
• curprev 11:3511:35, 21 July 2014‎ Katrina Sherbina talk contribs‎ 30,784 bytes +5‎ →‎Create MA Plots and Box Plots for the GCAT Chips: Corrected the name of a variable
• curprev 11:3411:34, 21 July 2014‎ Kam D. Dahlquist talk contribs‎ 30,779 bytes +84‎ →‎Create MA Plots and Box Plots for the GCAT Chips: added that NaN warning OK
• curprev 11:3311:33, 21 July 2014‎ Kam D. Dahlquist talk contribs‎ 30,695 bytes +152‎ →‎Between Array Normalization of Only Ontario Chip Data: extra note that this is not for combining GCAT and Ontario data
• curprev 11:1511:15, 21 July 2014‎ Katrina Sherbina talk contribs‎ 30,543 bytes +293‎ →‎Input Files for R: Added a description of the microarray chips normalized

1 May 2014

• curprev 16:4616:46, 1 May 2014‎ Kam D. Dahlquist talk contribs‎ 30,250 bytes +37‎ →‎Within Array Normalization for the Ontario Chips: hit enter with every line of code
• curprev 16:4516:45, 1 May 2014‎ Kam D. Dahlquist talk contribs‎ 30,213 bytes −2‎ →‎Data Normalization: slight rephrase
• curprev 16:4416:44, 1 May 2014‎ Kam D. Dahlquist talk contribs‎ 30,215 bytes −124‎ →‎Create a targets file with information about the .gpr files: clarified that it is the MasterList for the sequence of chips
• curprev 16:2616:26, 1 May 2014‎ Kam D. Dahlquist talk contribs‎ 30,339 bytes +6‎ →‎Data Normalization: fixed formatting and phrasing for S. paradoxus
• curprev 16:2416:24, 1 May 2014‎ Kam D. Dahlquist talk contribs‎ 30,333 bytes +126‎ →‎Create a targets file with information about the .gpr files: slight grammatical fix, specified columns by A, B, C, etc.
• curprev 16:1816:18, 1 May 2014‎ Kam D. Dahlquist talk contribs‎ 30,207 bytes +777‎ note on versions of R/limma package and how to install

29 April 2014

• curprev 14:4314:43, 29 April 2014‎ Katrina Sherbina talk contribs‎ 29,430 bytes +3‎ →‎Within Array Normalization for the GCAT Chips: Changed formatting of bullets with bolded text
• curprev 14:4214:42, 29 April 2014‎ Katrina Sherbina talk contribs‎ 29,427 bytes +6‎ →‎Within Array Normalization for the GCAT Chips: Preceded the description of the GCAT chp gene name correction with "NOTE:"
• curprev 14:4114:41, 29 April 2014‎ Katrina Sherbina talk contribs‎ 29,421 bytes +648‎ →‎Within Array Normalization for the GCAT Chips: Added description of how to remove "_01" if it appears at the end of gene names in the GPR files from the GCAT chips.
• curprev 14:3914:39, 29 April 2014‎ Katrina Sherbina talk contribs‎ 28,773 bytes 0‎ →‎Within Array Normalization for the GCAT Chips: Made a correction to the description of the colnames and rownames of MG2.
• curprev 13:1413:14, 29 April 2014‎ Katrina Sherbina talk contribs‎ 28,773 bytes +336‎ →‎Between Array Normalization of Only Ontario Chip Data: Changed the protocol in order to reorder the columns of the normalized data matrix according to the MasterList specified in the targets file
• curprev 13:0413:04, 29 April 2014‎ Katrina Sherbina talk contribs‎ 28,437 bytes −4‎ →‎Between Array Normalization of Only Ontario Chip Data

19 August 2013

• curprev 14:1614:16, 19 August 2013‎ Katrina Sherbina talk contribs‎ 28,441 bytes +38‎ →‎Create MA Plots and Box Plots for the Ontario Chips: Replaced readline() call with browser() call in the for loop to generate box plots.
• curprev 13:4713:47, 19 August 2013‎ Katrina Sherbina talk contribs‎ 28,403 bytes +56‎ →‎Create MA Plots and Box Plots for the Ontario Chips: Changed the readline() call to the call browser()

29 May 2013

• curprev 21:4321:43, 29 May 2013‎ Katrina Sherbina talk contribs‎ 28,347 bytes +222‎ →‎Create MA Plots and Box Plots for the Ontario Chips: Added more information regarding the box plot for loop.
• curprev 21:2621:26, 29 May 2013‎ Katrina Sherbina talk contribs‎ 28,125 bytes −1‎ →‎Between Array Normalization of Only Ontario Chip Data: Added the first and last line of code (in the outlined boxes).
• curprev 21:2521:25, 29 May 2013‎ Katrina Sherbina talk contribs‎ 28,126 bytes +84‎ →‎Between Array Normalization of Only Ontario Chip Data: Added more information to the last bullet.
• curprev 21:2521:25, 29 May 2013‎ Katrina Sherbina talk contribs‎ 28,042 bytes +84‎ →‎Between Array Normalization of Merged GCAT and Ontario Chip Data: Added more information to the last bullet.
• curprev 21:2421:24, 29 May 2013‎ Katrina Sherbina talk contribs‎ 27,958 bytes +84‎ →‎Within Array Normalization for the GCAT Chips: Added more to the last bullet.
• curprev 21:2321:23, 29 May 2013‎ Katrina Sherbina talk contribs‎ 27,874 bytes +99‎ →‎Data Normalization: Added some more information.
• curprev 21:2121:21, 29 May 2013‎ Katrina Sherbina talk contribs‎ 27,775 bytes +1‎ →‎Between Array Normalization of Only Ontario Chip Data
• curprev 21:1521:15, 29 May 2013‎ Katrina Sherbina talk contribs‎ 27,774 bytes +1,508‎ →‎Between Array Normalization of Only Ontario Chip Data: Added code.

28 May 2013

• curprev 23:5223:52, 28 May 2013‎ Katrina Sherbina talk contribs‎ 26,266 bytes +1‎ →‎Create MA Plots and Box Plots for the GCAT Chips
• curprev 23:5123:51, 28 May 2013‎ Katrina Sherbina talk contribs‎ 26,265 bytes −1,635‎ →‎Create MA Plots and Box Plots for the Ontario Chips: Edited the lines of code.
• curprev 23:0923:09, 28 May 2013‎ Katrina Sherbina talk contribs‎ 27,900 bytes 0‎ →‎Create MA plots and Box Plots for the Ontario Chips: Corrected title.
• curprev 23:0923:09, 28 May 2013‎ Katrina Sherbina talk contribs‎ 27,900 bytes 0‎ →‎Create MA plots and Box Plots for the GCAT Chips: Corrected title.
• curprev 23:0823:08, 28 May 2013‎ Katrina Sherbina talk contribs‎ m 27,900 bytes −1‎ →‎Create MA plots and Box Plots for the GCAT Chips
• curprev 23:0723:07, 28 May 2013‎ Katrina Sherbina talk contribs‎ 27,901 bytes +49‎ →‎Visualize the Normalized Data: Edited the code in "Create MA plots and Box Plots for the GCAT Chips" section.

27 May 2013

• curprev 22:5722:57, 27 May 2013‎ Katrina Sherbina talk contribs‎ 27,852 bytes +199‎ →‎Within Array Normalization for the GCAT Chips: Added line of code.

23 May 2013

• curprev 16:0016:00, 23 May 2013‎ Katrina Sherbina talk contribs‎ 27,653 bytes −53‎ →‎Visualize the Normalized Data: Edited description about MA plot.
• curprev 15:5015:50, 23 May 2013‎ Katrina Sherbina talk contribs‎ 27,706 bytes +85‎ →‎Visualize the Normalized Data: Added information to the first subsection.
• curprev 15:4515:45, 23 May 2013‎ Katrina Sherbina talk contribs‎ 27,621 bytes +50‎ →‎Between Array Normalization of Merged GCAT and Ontario Chip Data: Expanded the last bullet.
• curprev 15:4215:42, 23 May 2013‎ Katrina Sherbina talk contribs‎ 27,571 bytes +44‎ →‎Within Array Normalization for the Ontario Chips: Added more description about the code.
• curprev 15:4215:42, 23 May 2013‎ Katrina Sherbina talk contribs‎ 27,527 bytes +264‎ →‎Within Array Normalization for the GCAT Chips: Added more description about the code.
• curprev 15:4115:41, 23 May 2013‎ Katrina Sherbina talk contribs‎ 27,263 bytes +236‎ →‎Within Array Normalization for the Ontario Chips: Added more description about the code.
• curprev 15:3515:35, 23 May 2013‎ Katrina Sherbina talk contribs‎ m 27,027 bytes −6‎ →‎Visualizing the Normalized Data: Edited section names.
• curprev 15:3515:35, 23 May 2013‎ Katrina Sherbina talk contribs‎ 27,033 bytes +304‎ →‎Generating MA Plots and Boxplots: Added subsections and a brief description of the plots.
• curprev 15:0715:07, 23 May 2013‎ Katrina Sherbina talk contribs‎ 26,729 bytes +910‎ →‎Within Array Normalization for the GCAT Chips: Added lines of code from another section.
• curprev 15:0615:06, 23 May 2013‎ Katrina Sherbina talk contribs‎ 25,819 bytes −903‎ →‎Between Array Normalization of Merged GCAT and Ontario Chip Data: Took out code.
• curprev 15:0315:03, 23 May 2013‎ Katrina Sherbina talk contribs‎ 26,722 bytes −148‎ →‎Between Array Normalization of Merged GCAT and Ontario Chip Data: Edited code.
• curprev 14:4714:47, 23 May 2013‎ Katrina Sherbina talk contribs‎ 26,870 bytes −2‎ →‎Within Array Normalization for the GCAT Chips: Edited code.
• curprev 14:4014:40, 23 May 2013‎ Katrina Sherbina talk contribs‎ 26,872 bytes +2‎ →‎Within Array Normalization for the Ontario Chips: Edited code.

22 May 2013

• curprev 17:4417:44, 22 May 2013‎ Katrina Sherbina talk contribs‎ 26,870 bytes +253‎ →‎Between Array Normalization of Merged GCAT and Ontario Chip Data: Added code.
• curprev 17:2617:26, 22 May 2013‎ Katrina Sherbina talk contribs‎ 26,617 bytes +332‎ →‎Within Array Normalization for the GCAT Chips: Added information about which section to proceed to next.
• curprev 17:1817:18, 22 May 2013‎ Katrina Sherbina talk contribs‎ 26,285 bytes +163‎ →‎Create a targets file with information about the .gpr files: Corrected listing of columns.
• curprev 17:0917:09, 22 May 2013‎ Katrina Sherbina talk contribs‎ 26,122 bytes +119‎ →‎Between Array Normalization of Merged GCAT and Ontario Chip Data: Edited the code.
• curprev 16:4116:41, 22 May 2013‎ Katrina Sherbina talk contribs‎ 26,003 bytes +440‎ →‎Within Array Normalization for the GCAT Chips: Added code.
• curprev 16:3516:35, 22 May 2013‎ Katrina Sherbina talk contribs‎ 25,563 bytes +219‎ →‎Create a targets file with information about the .gpr files: Added more information about the targets file for the GCAT chips.
• curprev 16:2816:28, 22 May 2013‎ Katrina Sherbina talk contribs‎ 25,344 bytes +498‎ →‎Data Normalization: Edited code in the section "Within Array Normalization for the GCAT Chips"; switched the code in the last two subsections of this section.
• curprev 13:2213:22, 22 May 2013‎ Katrina Sherbina talk contribs‎ 24,846 bytes +7‎ →‎Data Normalization: Modified code within "Within Array Normalization for the Ontario Chips" section.

21 May 2013

• curprev 17:3617:36, 21 May 2013‎ Katrina Sherbina talk contribs‎ 24,839 bytes 0‎ →‎Data Normalization: Fixed a link.
• curprev 17:3517:35, 21 May 2013‎ Katrina Sherbina talk contribs‎ 24,839 bytes +585‎ Added a new section to introduce the normalization protocol.
• curprev 17:1217:12, 21 May 2013‎ Katrina Sherbina talk contribs‎ m 24,254 bytes −4‎ →‎Within Array Normalization of the Ontario Chip Data
• curprev 17:1117:11, 21 May 2013‎ Katrina Sherbina talk contribs‎ m 24,258 bytes +4‎ →‎Within Array Normalization of the Ontario Chip Data: Edited the names of the links that appear.
• curprev 17:1017:10, 21 May 2013‎ Katrina Sherbina talk contribs‎ m 24,254 bytes 0‎ →‎Within Array Normalization of the Ontario Chip Data: Fixed an awkward space.
• curprev 17:0917:09, 21 May 2013‎ Katrina Sherbina talk contribs‎ 24,254 bytes +150‎ →‎Within Array Normalization of the Ontario Chip Data: Added a link to the end of the section.
• curprev 17:0617:06, 21 May 2013‎ Katrina Sherbina talk contribs‎ 24,104 bytes +66‎ Added sections and revised names of some existing section.
• curprev 16:5916:59, 21 May 2013‎ Katrina Sherbina talk contribs‎ 24,038 bytes +856‎ →‎Within Array Normalization for the Ontario Chips: Edited content and added an internal link.
• curprev 16:1816:18, 21 May 2013‎ Katrina Sherbina talk contribs‎ m 23,182 bytes 0‎ →‎Create a targets file with information about the .gpr files: Corrected file extension
• curprev 16:1816:18, 21 May 2013‎ Katrina Sherbina talk contribs‎ 23,182 bytes +230‎ →‎Create a targets file with information about the .gpr files: Added information on saving the targets files.
• curprev 14:2414:24, 21 May 2013‎ Katrina Sherbina talk contribs‎ 22,952 bytes −3,067‎ Deleted a section "Create a file with the gene IDs for each chip"; edited title of first section
• curprev 12:4112:41, 21 May 2013‎ Katrina Sherbina talk contribs‎ m 26,019 bytes +116‎ →‎Create a targets file With information about the .gpr files: Fixed some grammar mistakes.

20 May 2013

• curprev 19:0019:00, 20 May 2013‎ Katrina Sherbina talk contribs‎ 25,903 bytes +2,448‎ →‎Creating the Input Files: Began to divide the section into subsections. Added more detail about creating the targets file.
• curprev 17:2417:24, 20 May 2013‎ Katrina Sherbina talk contribs‎ 23,455 bytes +34‎ Revised the first sentence to include what kinds of chips have been normalized.
• curprev 15:2615:26, 20 May 2013‎ Katrina Sherbina talk contribs‎ 23,421 bytes +236‎ Added links to download software for normalization.
• curprev 14:4914:49, 20 May 2013‎ Katrina Sherbina talk contribs‎ 23,185 bytes −2,862‎ Deleted Section Title "Alternate Way to Filter GCAT Chips"
• curprev 14:4714:47, 20 May 2013‎ Katrina Sherbina talk contribs‎ m 26,047 bytes +5‎ →‎Within Array Normalization of GCAT Chips: Edited section name.
• curprev 14:4614:46, 20 May 2013‎ Katrina Sherbina talk contribs‎ 26,042 bytes +169‎ Divided the directions into different sections

5 June 2012

• curprev 17:1217:12, 5 June 2012‎ Katrina Sherbina talk contribs‎ 25,873 bytes +2‎ →‎Alternate Way to Filter GCAT Chips: Indented rownames and colnames lines of code so that the reader knows that they are lines of code.
• curprev 16:2316:23, 5 June 2012‎ Katrina Sherbina talk contribs‎ 25,871 bytes −1‎ →‎Normalizing the Data: Corrected the RG line so that the first column of Targets is used not the first row first column.

1 November 2011

• curprev 15:5015:50, 1 November 2011‎ Katrina Sherbina talk contribs‎ 25,872 bytes +394‎ →‎Normalizing the Data: Addressed how to replace "NA's" in the GCAT data in the .csv file.

18 October 2011

• curprev 16:4116:41, 18 October 2011‎ Katrina Sherbina talk contribs‎ 25,478 bytes +578‎ →‎Generating MA Plots and Boxplots: Modified code for making boxplots after within array and scale normalization.

11 October 2011

• curprev 19:5119:51, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 24,900 bytes +5‎ →‎Alternate Way to Filter GCAT Chips: Edited procedure after importing CSV with ordered headers.
• curprev 19:4119:41, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 24,895 bytes −123‎ →‎Alternate Way to Filter GCAT Chips: Edited subsetting, binding, sorting, and merging directions.
• curprev 18:4318:43, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 25,018 bytes −4‎ →‎Alternate Way to Filter GCAT Chips: Edted sorting and subsetting directions.
• curprev 18:0918:09, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 25,022 bytes +15‎ →‎Normalizing the Data: Renamed the last file exported from R with all of the normalized data.
• curprev 18:0718:07, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 25,007 bytes 0‎ →‎Normalizing the Data: Edited procedure for how to deal with GCAT chips and to merge GCAT and Ontario data.
• curprev 17:4317:43, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 25,007 bytes +4‎ →‎Normalizing the Data: Edited designation of variable "row".
• curprev 17:4117:41, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 25,003 bytes −94‎ →‎Normalizing the Data: Edited how to create files with the gene IDs.
• curprev 17:1017:10, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 25,097 bytes −3‎ →‎Normalizing the Data: Edited procedure for importing files relating to the Ontario chips.
• curprev 17:0517:05, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 25,100 bytes −2‎ →‎Normalizing the Data
• curprev 17:0417:04, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 25,102 bytes 0‎ →‎Normalizing the Data: Edited discussion about creating CSV files for the GCAT and Ontario gene IDs.
• curprev 16:5916:59, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 25,102 bytes +245‎ →‎Normalizing the Data: Edited discussion about how to create gene ID CSV file for GCAT chips.
• curprev 16:3916:39, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 24,857 bytes +88‎ →‎Normalizing the Data: Edited discussion about creating csv file with gene ID's.
• curprev 16:1916:19, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 24,769 bytes +7‎ →‎Alternate Way to Filter GCAT Chips: Changed variables, need to confirm
• curprev 15:4815:48, 11 October 2011‎ Nicholas A. Rohacz talk contribs‎ 24,762 bytes −6‎ →‎Alternate Way to Filter GCAT Chips

21 July 2011

• curprev 12:4712:47, 21 July 2011‎ Katrina Sherbina talk contribs‎ 24,768 bytes +2,891‎ →‎Normalizing the Data: Added protocol for an alternate way to filter GCAT Chips.
• curprev 11:4311:43, 21 July 2011‎ Katrina Sherbina talk contribs‎ 21,877 bytes +1,375‎ Finished writing about how to modify the code when working with different strains.
• curprev 10:2610:26, 21 July 2011‎ Katrina Sherbina talk contribs‎ 20,502 bytes +382‎ Began protocol for how to change the code when moving on from strain to strain.
• curprev 10:1210:12, 21 July 2011‎ Katrina Sherbina talk contribs‎ 20,120 bytes +1,658‎ →‎Generating MA Plots and Boxplots: Added protocol on how to generate boxplots for Ontario chips.

20 July 2011

• curprev 17:1117:11, 20 July 2011‎ Katrina Sherbina talk contribs‎ 18,462 bytes +4,854‎ Added protocol for creating MA plots for the Ontario chips.
• curprev 16:4716:47, 20 July 2011‎ Katrina Sherbina talk contribs‎ 13,608 bytes +1,897‎ Wrote up protocol for how to generate boxplots for GCAT data.
• curprev 16:3516:35, 20 July 2011‎ Katrina Sherbina talk contribs‎ 11,711 bytes +3,412‎ Wrote up protocol for how to generate MA plots for GCAT data.

15 July 2011

• curprev 14:2314:23, 15 July 2011‎ Nicholas A. Rohacz talk contribs‎ 8,299 bytes +87‎ corrected small grammatical problems
• curprev 14:1414:14, 15 July 2011‎ Nicholas A. Rohacz talk contribs‎ 8,212 bytes −12,304‎ updated the R tutorial and code to process microarray data

8 July 2011

• curprev 11:2511:25, 8 July 2011‎ Katrina Sherbina talk contribs‎ 20,516 bytes −73‎ →‎Normalizing the Data: Deleted extra line of code in making matrix for GCAT chip data.
• curprev 11:0211:02, 8 July 2011‎ Katrina Sherbina talk contribs‎ 20,589 bytes +349‎ →‎Normalizing the Data: Changed code for creating blank matrices for Ontario and GCAT chips.

7 July 2011

• curprev 16:4216:42, 7 July 2011‎ Katrina Sherbina talk contribs‎ 20,240 bytes +56‎ →‎Normalizing the Data: Added more to intructions on what to do with the file after normalized GCAT data has been put through Access.
• curprev 14:0614:06, 7 July 2011‎ Katrina Sherbina talk contribs‎ 20,184 bytes +5,257‎ →‎Generating MA Plots and Box Plots: Added protocol on how to generate MA plots and box plots for GCAT chips. Also, edited earlier protocol for Ontario chips.
• curprev 13:3913:39, 7 July 2011‎ Katrina Sherbina talk contribs‎ 14,927 bytes +101‎ →‎Generating MA Plots and Box Plots: Made grammar corrections
• curprev 12:3512:35, 7 July 2011‎ Katrina Sherbina talk contribs‎ 14,826 bytes +3,117‎ →‎Generating MA Plots and Box Plots: Wrote protocol for generating MA plots and box plots for the ontario chip data.
• curprev 12:1712:17, 7 July 2011‎ Katrina Sherbina talk contribs‎ 11,709 bytes −1‎ →‎Generating MA Plots and Box Plots: Adjusted spacing between description and set of code.
• curprev 12:1712:17, 7 July 2011‎ Katrina Sherbina talk contribs‎ 11,710 bytes +3,696‎ →‎Generating MA Plots and Box Plots: Wrote the protocol for generating MA plots for the ontario chip data.
• curprev 11:5211:52, 7 July 2011‎ Katrina Sherbina talk contribs‎ 8,014 bytes +630‎ Added how to get the gene ID names from R. Added headers.

6 July 2011

• curprev 15:1715:17, 6 July 2011‎ Katrina Sherbina talk contribs‎ 7,384 bytes +13‎ Changed the variable names in some of the lines of code.
• curprev 12:2812:28, 6 July 2011‎ Katrina Sherbina talk contribs‎ 7,371 bytes 0‎ Made a correction to the last line of code.
• curprev 09:5709:57, 6 July 2011‎ Katrina Sherbina talk contribs‎ 7,371 bytes +24‎ Further edited the protocol.
• curprev 09:5609:56, 6 July 2011‎ Katrina Sherbina talk contribs‎ 7,347 bytes +1,725‎ Further edited the protocol.
• curprev 09:4709:47, 6 July 2011‎ Katrina Sherbina talk contribs‎ 5,622 bytes +1,330‎ Continued editing the protocol.
• curprev 09:3509:35, 6 July 2011‎ Katrina Sherbina talk contribs‎ 4,292 bytes +4,171‎ Began writing the protocal.
• curprev 09:1809:18, 6 July 2011‎ Kam D. Dahlquist talk contribs‎ 121 bytes +24‎ added template to page

5 July 2011

• curprev 11:0211:02, 5 July 2011‎ Kam D. Dahlquist talk contribs‎ 97 bytes +97‎ started page