Difference between revisions of "Johnllopez Week 10"
From LMU BioDB 2017
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===Preparing My Microarray Data File for Loading into STEM=== | ===Preparing My Microarray Data File for Loading into STEM=== | ||
#I started this portion by downloading [[Media: JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zip | the following]] spreadsheets. I added a new worksheet named dSWI4_stem, selected the values from dSWI4_ANOVA, and copied them into the new worksheet. | #I started this portion by downloading [[Media: JL BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017.zip | the following]] spreadsheets. I added a new worksheet named dSWI4_stem, selected the values from dSWI4_ANOVA, and copied them into the new worksheet. | ||
| − | #I modified this further by renaming the header "Master_Index" column to "SPOT", "ID" to " | + | #I modified this further by renaming the header "Master_Index" column to "SPOT", "ID" to "Gene Symbol", and deleting the "Standard_Name" column. |
| − | #I filtered the data on the B-H corrected p-value column to be greater than 0.05. | + | #I filtered the data on the B-H corrected p-value column to be greater than 0.05, and deleted all the data in the header row. Once I undid the filter, this ensured that all of the genes within the data set would have a B-H corrected p-value of <.05. The result was 2794 genes remaining. |
| + | #I then deleted all of the columns except for the Average Log Fold change columns at the timepoints. This would be used for [insert use] later on. | ||
| + | #I saved the spreadsheets as usal, then I saved it as a .txt file, which you can see [insert here]. | ||
| + | |||
===Downloading and Extracting STEM Software=== | ===Downloading and Extracting STEM Software=== | ||
Revision as of 18:21, 6 November 2017
Electronic Lab Notebook
Preparing My Microarray Data File for Loading into STEM
- I started this portion by downloading the following spreadsheets. I added a new worksheet named dSWI4_stem, selected the values from dSWI4_ANOVA, and copied them into the new worksheet.
- I modified this further by renaming the header "Master_Index" column to "SPOT", "ID" to "Gene Symbol", and deleting the "Standard_Name" column.
- I filtered the data on the B-H corrected p-value column to be greater than 0.05, and deleted all the data in the header row. Once I undid the filter, this ensured that all of the genes within the data set would have a B-H corrected p-value of <.05. The result was 2794 genes remaining.
- I then deleted all of the columns except for the Average Log Fold change columns at the timepoints. This would be used for [insert use] later on.
- I saved the spreadsheets as usal, then I saved it as a .txt file, which you can see [insert here].
