Dwilliams Project Notebook

Week 12

Electronic Lab Notebook

Went to the Arrayexpress website and downloaded all of the microarray raw data. Proceeded to upload all of the microarray raw data onto team wiki page. I also opened the raw data in an excel spreadsheet and begin determining gene ID's and future formatting for the statistical analysis that we will perform on our species next week.

Reflection

1. What were the week’s key accomplishments?
   • We worked efficiently and effectively in our group when preparing the powerpoint presentation. As an individual, I worked on uploading the microarray data to the team page.
2. What are next week’s target accomplishments?
   • Next week I would like to finish our formatting of the microarray data and begin our statistical analysis.
3. What team strengths were seen this week?
   • We worked well as a group and held a good level of communication with each other throughout the process.
4. What team weaknesses were seen this week?
   • We weren't as organized as we could have been, although I think that this is something that we will definitely improve upon in the future.

Week 13

Electronic Lab Notebook

• Downloaded Affymetrix software from dChip web site.
• Saved Affymetrix software into downnloads on desktop of computer (front row, 3 over from the right).
• Clicked on tutorial hyperlink from dChip web site.
• Opened "dChip expression data analysis" word doc.
• Begin following steps from word doc.:
  • Obtained dChip and Microarray Data
  1. Downloaded and unzipped Microarray Data from ArrayExpress website.
  2. Specifically, Media: Raw_Data_DW_V1_12112013_E-GEOD-39530.raw.1.zip.
  • Basic steps to open expression data
  1. Opened dChip software.
  2. Clicked "Analysis"-->"Open Group".
  3. Specified data directory as CEL file.
  4. Selected working directory in "Options".
  5. Selected following specifications and ran dChip:
  6. 
  7. 
  8. 
  9. Placed .cdfin file in folder to run dChip.exe
  10. Select analysis--> Normalize and Model Data
  11. Process each graph and hit "ok".
  12. Tools-->"Export Expression Value"
  13. Select all expression values-->run program-->find where file is saved.
  14. Open file in .xls format-->name file "Master Spreadsheet".
  • Renaming Columns in Master Spreadsheet
  1. Access sdrf file from team page.
  2. Save link as.
  3. Open using excel spreadsheet.
  4. Match gene ID's to gene ID's found in Master Spreadsheet columns to rename the number sequences with meaningful titles; e.g. "Gene expression data from_RB grown in axenic media + rifampicin rep 4"
  5. Separate into 5 groups.
  6. Find average of each group.
  7. Perform TTEST ((=TTEST(rangegroup1,rangegroup2,2,3))
  8. Find EB to RB without rifampicin.
  9. Find EB to RB with rifampicin.
  10. Find Log Value (EB/RB) with/without rifampicin.