Difference between revisions of "Rlegaspi Week 12"

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(→‎Raw Data Files (Cy3 and Cy5 files): Link page to raw data files. Taking a break and then continue with rest of las=tss)
(→‎Raw Data Files (Cy3 and Cy5 files): Finished uploading and linking raw data files.)
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*C20_3_Cy3: [[File:GSM496746 MR-1 C20 3 Cy3.xlsx]]
 
*C20_3_Cy3: [[File:GSM496746 MR-1 C20 3 Cy3.xlsx]]
 
*C20_3_Cy5: [[File:GSM496746 MR-1 C20 3 Cy5.xlsx]]
 
*C20_3_Cy5: [[File:GSM496746 MR-1 C20 3 Cy5.xlsx]]
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*C20_4_Cy3: [[]]
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*C20_4_Cy3: [[File:GSM496747 MR-1 C20 4 Cy3.xlsx]]
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*C20_4_Cy5: [[]]
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*C20_4_Cy5: [[File:GSM496747 MR-1 C20 4 Cy5.xlsx]]
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*C40_1_Cy3: [[]]
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*C40_1_Cy3: [[File:GSM496748 MR-1 C40 1 Cy3.xlsx]]
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*C40_1_Cy5: [[]]
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*C40_1_Cy5: [[File:GSM496748 MR-1 C40 1 Cy5.xlsx]]
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*C40_2_Cy3: [[]]
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*C40_2_Cy3: [[File:GSM496749 MR-1 C40 2 Cy3.xlsx]]
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*C40_2_Cy5: [[]]
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*C40_2_Cy5: [[File:GSM496749 MR-1 C40 2 Cy5.xlsx]]
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*C40_3_Cy3: [[]]
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*C40_3_Cy3: [[File:GSM496750 MR-1 C40 3 Cy3.xlsx]]
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*C40_3_Cy5: [[]]
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*C40_3_Cy5: [[File:GSM496750 MR-1 C40 3 Cy5.xlsx]]
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*C40_4_Cy3: [[]]
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*C40_4_Cy3: [[File:GSM496751 MR-1 C40 4 Cy3.xlsx]]
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*C40_4_Cy5: [[]]
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*C40_4_Cy5: [[File:GSM496751 MR-1 C40 4 Cy5.xlsx]]
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*C60_1_Cy3: [[]]
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*C60_1_Cy3: [[File:GSM496752 MR-1 C60 1 Cy3.xlsx]]
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*C60_1_Cy5: [[]]
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*C60_1_Cy5: [[File:GSM496752 MR-1 C60 1 Cy5.xlsx]]
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*C60_2_Cy3: [[]]
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*C60_2_Cy3: [[File:GSM496753 MR-1 C60 2 Cy3.xlsx]]
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*C60_2_Cy5: [[]]
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*C60_2_Cy5: [[File:GSM496753 MR-1 C60 2 Cy5.xlsx]]
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*C60_3_Cy3: [[]]
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*C60_3_Cy3: [[File:GSM496754 MR-1 C60 3 Cy3.xlsx]]
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*C60_3_Cy5: [[]]
+
*C60_3_Cy5: [[File:GSM496754 MR-1 C60 3 Cy5.xlsx]]
−
*C60_4_Cy3: [[]]
+
*C60_4_Cy3: [[File:GSM496755 MR-1 C60 4 Cy3.xlsx]]
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*C60_4_Cy5: [[]]
+
*C60_4_Cy5: [[File:GSM496755 MR-1 C60 4 Cy5.xlsx]]
  
 
== Consolidating Files ==
 
== Consolidating Files ==

Revision as of 05:32, 24 November 2015

HeavyMetal.jpg

Shewanella oneidensis

Our Gene Database Testing Report

Group Paper - File:Final Report 20151218 2 HMH.docx

Group Members

Important Links

Our Files

Our Deliverables

Gene Database Project Links
Overview Deliverables Reference Format Guilds Project Manager GenMAPP User Quality Assurance Coder
Teams Heavy Metal HaterZ The Class Whoopers GÉNialOMICS Oregon Trail Survivors
Individual Journal Entries
Mary Alverson Week 11 Week 12 Week 14 Week 15
Emily Simso Week 11 Week 12 Week 14 Week 15
Ron Legaspi Week 11 Week 12 Week 14 Week 15
Josh Kuroda Week 11 Week 12 Week 14 Week 15

GenMAPP User Milestones

Milestone 1: Startup from Original Microarray Paper and Data

  1. Download microarray data in its “rawest” form that you can find. (Consult with Dr. Dahlquist about this.)
  2. Verify that the gene IDs in the microarray data match the chosen species and strain that is being used to create the .gdb. (Needs to be done in conjunction with the QA and Coder.)
  3. File management: on your team's home page
    • Link to the source of the microarray data
    • Upload the microarray data files to the wiki

Milestone 2: Data Preparation

  1. Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
  2. Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
  3. Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
  4. Consult with Dr. Dahlquist on how to process the data (normalization, statistics)

Milestone 3: On-going Analysis Cycle

This milestone represents the on-going work of the GenMAPP user, as the project gradually converges toward a final version of its gene database and compares its own results to the results in the original microarray paper. (Note: These milestones may continue on to Week 13.)

  1. Perform the statistical analysis in Excel.
  2. Format the gene expression data for import into GenMAPP.
  3. Import data into GenMAPP, create ColorSets, and run MAPPFinder.
  4. Document and take notes on test runs with GenMAPP.
    • Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb.
  5. Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation.
  6. Create a .mapp file showing one pathway that is changed in your data.

Summary of Progress

Consultation for Data Processing

  • During the Thursday class period (11/19/2015), Dr. Dahlquist went over an interpretation of how the paper writers acquired microarray data; in addition, Dr. Dahlquist explained an approach we would need to take in order to extract and to process the raw data from the files in order to be used for normalization and statistical analysis.
    1. Dr. Dahlquist Notes:
      1. Page 1 - Media:DrDDataProcessNotes1 20151119 HMH.JPG
      2. Page 2 - Media:DrDDataProcessNotes2 20151119 HMH.JPG
  • Will work on all "C" files - Microarray data gathered from MR-1 cultures treated with iron chelator at different time intervals.
  • 52 chips total - 104 files (one for Cy3, one for Cy5)
  • Sample and Data Relationships File has 208 - Presence of duplicates.
  • Need columns G (Gene ID), K (Signal Median), L (Background Median), H (Flag Column)
  • Log2 (Cy5 signal median - Cy5 signal background / Cy3 signal median - Cy3 signal background) - Log Equation to be used with data

Data Processing

  • Downloaded each raw data file and stored files on flash drive.
  • Opened raw data files using Microsoft Excel.
  • Deleted unnecessary information at the top of the raw data columns; information was labeled as Header.
  • Created new tab with "Needed Columns" label
  • Transferred columns G, H, K, and L to this tab
  • Saved the file as a .xlsx file and uploaded to the wiki

Raw Data Files (Cy3 and Cy5 files)

Consolidating Files

  • Combined the Cy3 and Cy5 files for each time point onto a single spreadsheet
  • In each new spreadsheet:
    • Sheet 1 = Cy3
    • Sheet 2 = Cy5
    • Sheet 3 = Combined
      • Added _Cy3 to columns A-D and _Cy5 to columns E-H on row titles to differentiate the samples
  • Calculated the Log2 for each of the following files in Sheet 4
    • Copied over all of the data from Combined sheet
    • Column I labeled (Cy5 signal median - Cy5 background median)
      • I2=G2-H2
    • Column J labeled (Cy3 signal median - Cy3 background median)
      • J2=C2-D2
    • Column K labeled (Cy5/Cy3)
      • K2=I2/J2
    • Column L labeled Log2
      • performed =LOG(K2, 2)


Ron Legaspi
BIOL 367, Fall 2015

Assignment Links
Individual Weekly Journals
Shared Weekly Journals
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