Difference between revisions of "Asandle1 Week 10"
(Copied in week 9 as an outline to edit. and made a few edits to ordering) |
(→Methods/Electronic Notebook: added notes from notebook) |
||
| Line 16: | Line 16: | ||
3) Renamed my left MasterIndex column to SPOT | 3) Renamed my left MasterIndex column to SPOT | ||
| − | 4)Renamed Column B to "Gene Symbol" | + | 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 <b>EXCEPT</b> for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.). | ||
| + | 10) Helped Charlotte do the same filtering step. She had a small issue where she deleted the data on the rows but not the rows. | ||
=Data and Files= | =Data and Files= | ||
Revision as of 13:48, 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
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 do the same filtering step. She had a small issue where she deleted the data on the rows but not the rows.
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
To User Page: User: Asandle1
To Template: Template:Asandle1
