Difference between revisions of "Bklein7 Week 8"

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==Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)==
 
==Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)==
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*Downloaded the [Merrell_Compiled_Raw_Data_Vibrio.xls] file.
 +
**Renamed the file to Merrell_Compiled_Raw_Data_Vibrio_BK_20151015.xls
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===Normalizing the log ratios for the set of slides in the experiment===
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*Copied data from the ''compiled_raw_data'' tab to a new tab, entitled ''scaled_centered''
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**Inserted two rows below the ''ID'' row, labelled ''Average'' and ''StDev''.
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***''Average'': Calculated the averages of the data in each column using the function <code>=AVERAGE()</code>
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****Sample- for row B the function is <code>=AVERAGE(B4:B5224)</code>
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***''StDev'': Calculated the standard deviations of the data in each column using the function <code>=STDEV()</code>
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****Sample- for row B the function is <code>=STDEV(B4:B5224)</code>
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**Created a new series of columns for data sets A1-C4, adding the labels "_scaled_centered" (e.g. A1_scaled_centered)
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***Wrote a function to normalize each value in the data set
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****For the first value in column B (data set A1), the function was <code>=(B4-B$2)/B$3</code>
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****Extended this to all data values in the new ''scaled_centered'' columns
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*Created a new tab entitled ''statistics''
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**Copied over:
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***The first column of gene ''ID'' values from the ''compiled_raw_data'' tab
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***The ''_scaled_centered'' columns from the ''scaled_centered'' tab
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**Deleted the blank ''Average'' and ''StDev'' rows
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**Created a new series of columns
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*COPY FROM OPENWETWARE FOR ELECTRONIC LAB NOTEBOOK
  
 
==MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2)==
 
==MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2)==

Revision as of 22:45, 15 October 2015

Overview of Microarray Data Analysis

Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)

  • Downloaded the [Merrell_Compiled_Raw_Data_Vibrio.xls] file.
    • Renamed the file to Merrell_Compiled_Raw_Data_Vibrio_BK_20151015.xls

Normalizing the log ratios for the set of slides in the experiment

  • Copied data from the compiled_raw_data tab to a new tab, entitled scaled_centered
    • Inserted two rows below the ID row, labelled Average and StDev.
      • Average: Calculated the averages of the data in each column using the function =AVERAGE()
        • Sample- for row B the function is =AVERAGE(B4:B5224)
      • StDev: Calculated the standard deviations of the data in each column using the function =STDEV()
        • Sample- for row B the function is =STDEV(B4:B5224)
    • Created a new series of columns for data sets A1-C4, adding the labels "_scaled_centered" (e.g. A1_scaled_centered)
      • Wrote a function to normalize each value in the data set
        • For the first value in column B (data set A1), the function was =(B4-B$2)/B$3
        • Extended this to all data values in the new scaled_centered columns
  • Created a new tab entitled statistics
    • Copied over:
      • The first column of gene ID values from the compiled_raw_data tab
      • The _scaled_centered columns from the scaled_centered tab
    • Deleted the blank Average and StDev rows
    • Created a new series of columns
  • COPY FROM OPENWETWARE FOR ELECTRONIC LAB NOTEBOOK

MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2)

Conclusion

Links

Assignments Pages

Individual Journal Entries

Shared Journal Entries

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