Johnllopez Week 10

Electronic Lab Notebook

Preparing My Microarray Data File for Loading into STEM

1. 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.
2. I modified this further by renaming the header "Master_Index" column to "SPOT", "ID" to "Gene Symbol", and deleting the "Standard_Name" column.
3. 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.
4. 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.
5. 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.
6. I saved the spreadsheets as usual, then I saved it as a .txt file, which you can see [insert here].