Emilysimso Week 12

Goals

• Normalize data, statistical analysis of raw data

File Notes

• Will work on all "F" files
• 52 chips total - 104 files (one for Cy3, one for Cy5)
• sdrf file has 208 - duplicates
• Need columns G, K, L, H
• Log2 (Cy5 signal median-Cy5 signal background / Cy3 signal median - Cy3 signal background)

Files

Choosing Appropriate Columns

• Downloaded each raw data file
• Opened it using Xcel
• Deleted unnecessary information at the top of the raw data tab
• 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

• F1_1_Cy3: File:GSM496756 MR-1 F1 1 Cy3.xlsx
• F1_1_Cy5: File:GSM496756 MR-1 F1 1 Cy5.xlsx
• F1_2_Cy3: File:GSM496757 MR-1 F1 2 Cy3.xlsx
• F1_2_Cy5: File:GSM496757 MR-1 F1 2 Cy5.xlsx
• F1_3_Cy3: File:GSM496758 MR-1 F1 3 Cy3.xlsx
• F1_3_Cy5: File:GSM496758 MR-1 F1 3 Cy5.xlsx
• F1_4_Cy3: File:GSM496759 MR-1 F1 4 Cy3.xlsx
• F1_4_Cy5: File:GSM496759 MR-1 F1 4 Cy5.xlsx
• F5_1_Cy3: File:GSM496760 MR-1 F5 1 Cy3.xlsx
• F5_1_Cy5: File:GSM496760 MR-1 F5 1 Cy5.xlsx
• F5_2_Cy3: File:GSM496761 MR-1 F5 2 Cy3.xlsx
• F5_2_Cy5: File:GSM496761 MR-1 F5 2 Cy5.xlsx
• F5_3_Cy3: File:GSM496762 MR-1 F5 3 Cy3.xlsx
• F5_3_Cy5: File:GSM496762 MR-1 F5 3 Cy5.xlsx
• F5_4_Cy3: File:GSM496763 MR-1 F5 4 Cy3.xlsx
• F5_4_Cy5: File:GSM496763 MR-1 F5 4 Cy5.xlsx
• F10_1_Cy3: File:GSM496764 MR-1 F10 1 Cy3.xlsx
• F10_1_Cy5: File:GSM496764 MR-1 F10 1 Cy5.xlsx
• F10_2_Cy3: File:GSM496765 MR-1 F10 2 Cy3.xlsx
• F10_2_Cy5: File:GSM496765 MR-1 F10 2 Cy5.xlsx
• F10_3_Cy3: File:GSM496766 MR-1 F10 3 Cy3.xlsx
• F10_3_Cy5: File:GSM496766 MR-1 F10 3 Cy5.xlsx
• F10_4_Cy3: File:GSM496767 MR-1 F10 4 Cy3.xlsx
• F10_4_Cy5: File:GSM496767 MR-1 F10 4 Cy5.xlsx
• F20_1_Cy3: File:GSM496768 MR-1 F20 1 Cy3.xlsx
• F20_1_Cy5: File:GSM496768 MR-1 F20 1 Cy5.xlsx
• F20_2_Cy3: File:GSM496769 MR-1 F20 2 Cy3.xlsx
• F20_2_Cy5: File:GSM496769 MR-1 F20 2 Cy5.xlsx
• F20_3_Cy3: File:GSM496770 MR-1 F20 3 Cy3.xlsx
• F20_3_Cy5: File:GSM496770 MR-1 F20 3 Cy5.xlsx
• F20_4_Cy3: File:GSM496771 MR-1 F20 4 Cy3.xlsx
• F20_4:Cy5: File:GSM496771 MR-1 F20 4 Cy5.xlsx
• F40_1_Cy3: File:GSM496772 MR-1 F40 1 Cy3.xlsx
• F40_1_Cy5: File:GSM496772 MR-1 F40 1 Cy5.xlsx
• F40_2_Cy3: File:GSM496773 MR-1 F40 2 Cy3.xlsx
• F40_2_Cy5: File:GSM496773 MR-1 F40 2 Cy5.xlsx
• F40_3_Cy3: File:GSM496774 MR-1 F40 3 Cy3.xlsx
• F40_3_Cy5: File:GSM496774 MR-1 F40 3 Cy5.xlsx
• F40_4_Cy3: File:GSM496775 MR-1 F40 4 Cy3.xlsx
• F40_4:Cy5: File:GSM496775 MR-1 F40 4 Cy5.xlsx
• F60_1_Cy3: File:GSM496776 MR-1 F60 1 Cy3.xlsx
• F60_1_Cy5: File:GSM496776 MR-1 F60 1 Cy5.xlsx
• F60_2_Cy3: File:GSM496777 MR-1 F60 2 Cy3.xlsx
• F60_2_Cy5: File:GSM496777 MR-1 F60 2 Cy5.xlsx
• F60_3_Cy3: File:GSM496778 MR-1 F60 3 Cy3.xlsx
• F60_3_Cy5: File:GSM496778 MR-1 F60 3 Cy5.xlsx
• F60_4_Cy3: File:GSM496779 MR-1 F60 4 Cy3.xlsx
• F60_4:Cy5: File:GSM496779 MR-1 F60 4 Cy5.xlsx

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)

• File:F1 1 Combined.xlsx
• File:F1 2 Combined.xlsx
• File:F1 3 Combined.xlsx
• File:F1 4 Combined.xlsx
• File:F5 1 Combined.xlsx
• File:F5 2 Combined.xlsx
• File:F5 3 Combined.xlsx
• File:F5 4 Combined.xlsx
• File:F10 1 Combined.xlsx
• File:F10 2 Combined.xlsx
• File:F10 3 Combined.xlsx
• File:F10 4 Combined.xlsx
• File:F20 1 Combined.xlsx
• File:F20 2 Combined.xlsx
• File:F20 3 Combined.xlsx
• File:F20 4 Combined.xlsx
• File:F40 1 Combined.xlsx
• File:F40 2 Combined.xlsx
• File:F40 3 Combined.xlsx
• File:F40 4 Combined.xlsx
• File:F60 1 Combined.xlsx
• File:F60 2 Combined.xlsx
• File:F60 3 Combined.xlsx
• File:F60 4 Combined.xlsx

Weekly Assignment Information

User: Emilysimso

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Group Project

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