Difference between revisions of "Johnllopez Week 10"
From LMU BioDB 2017
(Elaborated further on Step 1) |
(Explained how I prepared the document for STEM) |
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#I modified this further by renaming the header "Master_Index" column to "SPOT", "ID" to "Gene Symbol", and deleting the "Standard_Name" column. | #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 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 | + | #I then deleted all of the columns except for the Average Log Fold change columns at the timepoints. I renamed the columns with just time and units. This would be used for analyzing the timepoints in STEM later on. |
| − | #I saved the spreadsheets as | + | #In addition, to avoid complications with the STEM software, I replaced any values with the error #DIV/0! with a blank string. There were 40 replacements made. |
| + | #I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [insert here]. | ||
Revision as of 18:28, 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. I renamed the columns with just time and units. This would be used for analyzing the timepoints in STEM later on.
- In addition, to avoid complications with the STEM software, I replaced any values with the error #DIV/0! with a blank string. There were 40 replacements made.
- I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [insert here].
