Difference between revisions of "Asandle1 Week 10"
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===Part 2: Using STEM=== | ===Part 2: Using STEM=== | ||
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| + | 1) I double clicked on stem.jar to run the program | ||
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| + | 2) STEM opened into the main interface window and I clicked on the Browse button to navigate to my file and select it. | ||
=Data and Files= | =Data and Files= | ||
Revision as of 14:09, 25 March 2024
Contents
Methods/Results/Electronic Notebook
Purpose
The purpose of this assignment is to get experience with the analysis part of the "data life cycle" for DNA microarray datasets and to "develop an intuition about different p-value cut-offs and their meanings.
It also is to show how to keep a detailed electronic lab notebook to make our research reproducible to develop an intuition about what different p-value cut-offs mean.
Methods/Electronic Notebook
Part 1: Data Setup and STEM Installation
1) I inserted a new worksheet into my Excel workbook and named it dGLN3_stem.
2) Selected all of the data from my dGLN3_ANOVA worksheet and pasted it as values into my new dGLN3_stem worksheet.
3) Renamed my left MasterIndex column to SPOT
4) Renamed Column B to "Gene Symbol".
5) Deleted the column named "Standard_Name".
6) Filtered the data on the B-H corrected p value to be > 0.05.
7) Selected all of the rows (except for the header) and deleted the rows by right-clicking and choosing "Delete Row" from the context menu.
8)Undid the filter.
9) Deleted all of the data columns EXCEPT for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
10) Helped Charlotte Kaplan do the same filtering step. She had a small issue where she deleted the data on the rows but not the rows.
11) Renamed the data columns with just the time and units (for example, 15m, 30m, etc.).
12) Helped Charlotte with Pasting Values.
13) There were some #DIV/0! errors. To fix, I am opening the Find/Replace dialog and searching for the DIV errors by #DIV/0!.
14) It removed 110 DIV/0’s.
15) Saved my work. Then used Save As to save it as .txt file.
16) I did not turn on file extensions because I am on a mac and it shows me already.
17) Tried to download the Stem software on mac but it was not a quick process so I moved to the Windows computer.
18) I used Box to upload the spreadsheet that I saved as a text file.
19) I downloaded the text file onto the windows computer.
20) I extracted it.
21) Dr. Dahlquist helped me turn on file extensions.
22) I downloaded and extracted the STEM software onto the computer.
23) I downloaded the Gene Ontology file gene_ontology.obo from https://lmu.box.com/s/t8i5s1z1munrcfxzzs7nv7q2edsktxgl
24) I downloaded the gene_association.sgd.gz file from https://lmu.box.com/s/zlr1s8fjogfssa1wl59d5shyybtm1d49
25) I put the files into the STEM folder that was created when I extracted all from the Stem.zip earlier.
Part 2: Using STEM
1) I double clicked on stem.jar to run the program
2) STEM opened into the main interface window and I clicked on the Browse button to navigate to my file and select it.
Data and Files
Media:AS&CK_BIOL367_S24_microarray-data_dGLN3.xlsx
Media:BIOL367_S24_Andrew_dGLN3_p-value_slide.pptx
Conclusion
I am not sure we have concluded this task yet. I think the conclusion will come with part 2.
Acknowledgements & References
Acknowledgments
- I worked on this assignment with Charlotte Kaplan in class. I helped her with a lot of her excel stuff because I had more experience. I texted her at 5:57 pm on wednesday about the p-values for B&H being strangely low for me. For the most part I did the assignment on my own and really was helping her catch up to me.
- Dr. Dahlquist was very helpful in class when I ran into some errors with the data. The specific errors are in the electronic notebook.
- I used the Week 9 instructions and followed them.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
18:04, 20 March 2024 (PDT)
References
- Dahlquist, K. Master_sheet_dGLN3.
- LMU BioDB 2024. (2024). Week 9. Retrieved Mar 20, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_9
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