Difference between revisions of "Emilysimso Week 12"
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***Added _Cy3 to columns A-D and _Cy5 to columns E-H on row titles to differentiate the samples | ***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 | *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 | ||
Revision as of 06:11, 20 November 2015
Contents
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
- 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
Assignments
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 13
- Week 14
- Week 15
Individual Journal Entries
- Emilysimso Week 2
- Emilysimso Week 3
- Emilysimso Week 4
- Emilysimso Week 5
- Emilysimso Week 6
- Emilysimso Week 7
- Emilysimso Week 8
- Emilysimso Week 9
- Emilysimso Week 10
- Emilysimso Week 11
- Emilysimso Week 12
- Emilysimso Week 13
- Emilysimso Week 14
- Emilysimso Week 15
Class Journal Entries
- Class Journal Week 1
- Class Journal Week 2
- Class Journal Week 3
- Class Journal Week 4
- Class Journal Week 5
- Class Journal Week 6
- Class Journal Week 7
- Class Journal Week 8
- Class Journal Week 9
- Class Journal Week 10
- Class Journal Week 11
- Class Journal Week 12
- Class Journal Week 13
- Class Journal Week 14
- Class Journal Week 15
