Difference between revisions of "Emilysimso Week 12"

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(Started uploading files)
 
(→‎Consolidating Files: notes to self)
 
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==Files==
 
==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_Cy3: [[File:GSM496756 MR-1 F1 1 Cy3.xlsx]]
 
*F1_1_Cy5: [[File:GSM496756 MR-1 F1 1 Cy5.xlsx]]
 
*F1_1_Cy5: [[File:GSM496756 MR-1 F1 1 Cy5.xlsx]]
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*F10_4_Cy5: [[File:GSM496767 MR-1 F10 4 Cy5.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_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]]
 +
 +
 +
 +
{{Template: Esimso entries etc}}

Latest revision as of 20:40, 20 November 2015

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


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)



Weekly Assignment Information

User: Emilysimso

Assignments

Individual Journal Entries

Class Journal Entries

Group Project

Heavy Metal HaterZ

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