Difference between revisions of "Data Analysts Week 13"
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With Quality Assurance [[User:Hivanson| Hailey Ivanson]] we downloaded and examined the microarray dataset, comparing it to the samples in our journal club article. We used the processed dataset from SGD. We made a sample-data relationship table that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number. | With Quality Assurance [[User:Hivanson| Hailey Ivanson]] we downloaded and examined the microarray dataset, comparing it to the samples in our journal club article. We used the processed dataset from SGD. We made a sample-data relationship table that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number. | ||
We came up with consistent column headers that summarize this information. We named each column CHP_LogFc_time-trial without using special characters. We organized the data in a worksheet in an Excel workbook so that: | We came up with consistent column headers that summarize this information. We named each column CHP_LogFc_time-trial without using special characters. We organized the data in a worksheet in an Excel workbook so that: | ||
| + | |||
-ID (GSE7645) is in the first column | -ID (GSE7645) is in the first column | ||
| + | |||
-Data columns are to the right, in increasing chronological order, using the column header pattern we created | -Data columns are to the right, in increasing chronological order, using the column header pattern we created | ||
| + | |||
-Treatments are grouped together | -Treatments are grouped together | ||
| + | |||
-Replicates are grouped together | -Replicates are grouped together | ||
| + | |||
-We deleted the "EWEIGHT" row and "GWEIGHT" column. | -We deleted the "EWEIGHT" row and "GWEIGHT" column. | ||
| + | |||
-We converted the data into Log2 fold changes (LogFC). | -We converted the data into Log2 fold changes (LogFC). | ||
| + | |||
-We undid log transformations before we calculated the ratios. | -We undid log transformations before we calculated the ratios. | ||
| + | |||
-We created new column headers and then transformed of all the data with the equation "=2^<cell designation>" | -We created new column headers and then transformed of all the data with the equation "=2^<cell designation>" | ||
| + | |||
-We computed the average value of the t0 timepoint for the control and CHP-treated data. | -We computed the average value of the t0 timepoint for the control and CHP-treated data. | ||
| + | |||
-We calculated the fold change by dividing each value for each timepoint by the average t0 value for the respective treatment (control or CHP-treated). | -We calculated the fold change by dividing each value for each timepoint by the average t0 value for the respective treatment (control or CHP-treated). | ||
| − | -We Log2 | + | |
| + | -We Log2 transformed the fold changes. | ||
-This procedure was adapted from [[Week 12]] LMU BioDB 2024. (2024). Week 12. Retrieved April 17, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_12 | -This procedure was adapted from [[Week 12]] LMU BioDB 2024. (2024). Week 12. Retrieved April 17, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_12 | ||
Revision as of 18:58, 17 April 2024
Charlotte and Katie's Data Analyst Journal
Milestone 1
-was completed as of April 11th when we gave our Journal Club Presentation with Hailey Ivanson
Milestone 2
With Quality Assurance Hailey Ivanson we downloaded and examined the microarray dataset, comparing it to the samples in our journal club article. We used the processed dataset from SGD. We made a sample-data relationship table that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number. We came up with consistent column headers that summarize this information. We named each column CHP_LogFc_time-trial without using special characters. We organized the data in a worksheet in an Excel workbook so that:
-ID (GSE7645) is in the first column
-Data columns are to the right, in increasing chronological order, using the column header pattern we created
-Treatments are grouped together
-Replicates are grouped together
-We deleted the "EWEIGHT" row and "GWEIGHT" column.
-We converted the data into Log2 fold changes (LogFC).
-We undid log transformations before we calculated the ratios.
-We created new column headers and then transformed of all the data with the equation "=2^<cell designation>"
-We computed the average value of the t0 timepoint for the control and CHP-treated data.
-We calculated the fold change by dividing each value for each timepoint by the average t0 value for the respective treatment (control or CHP-treated).
-We Log2 transformed the fold changes.
-This procedure was adapted from Week 12 LMU BioDB 2024. (2024). Week 12. Retrieved April 17, 2024 from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_12
