Difference between revisions of "Skinny Genes Quality Assurance"
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| − | + | ==Datas and Files== | |
| − | + | [[Media:Skinny Genes Editted Raw Data.xlsx | Skinny Genes Edited Raw Data]] | |
| − | [[ | ||
| − | |||
==Electronic Lab Notebook== | ==Electronic Lab Notebook== | ||
===Milestone 1=== | ===Milestone 1=== | ||
| + | *Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines | ||
===Milestone 2=== | ===Milestone 2=== | ||
| + | *Created presentation about the article | ||
| + | *We divided up the work into sections and each focused on our assigned task (each was designated a slide(s) and figure(s)) | ||
| + | *Also, worked on annotated bibliography | ||
===Milestone 3=== | ===Milestone 3=== | ||
| Line 17: | Line 19: | ||
===Milestone 4=== | ===Milestone 4=== | ||
| + | *The QAs worked on organizing the layout and naming the standard names and IDs. (Group worked alongside Prof. Dalquist due to complications) | ||
| + | *In essence, we put in a list of genes into the name translator and found ost of the IDs and standard names, but we had blanks for a good amount of genes. | ||
| + | *We used multiple websites which included: [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"], [http://llama.mshri.on.ca/synergizer/translate/ Synergizer], [https://rdrr.io/bioc/ClusterJudge/man/convert_Yeast_SGDId_2_systematic.html Bioconductor package] | ||
| + | *We recently received all the names to move on with our work. | ||
| + | *We spoke with other groups to ensure that column headers were consistent with how other groups structured the data. | ||
| + | *Deleted duplicate data under alias names | ||
| + | *Filled in missing gaps for names | ||
| + | |||
| + | ===Milestone 5=== | ||
| + | * | ||
| + | |||
| + | ===Problems=== | ||
| + | *Data set had duplicate data as well as alias for the duplicate data | ||
| + | *Many IDs/Standard names still were missing | ||
| + | *Manual input was needed to resolve (along with Prof. Dalquist) | ||
| + | '''Data was no fully complete and research and conversion was needed to move the database project along''' | ||
| + | |||
| + | ===Milestone 6=== | ||
| + | *made sure that all of the rows of data were imported into the database for the expression table | ||
| + | *made sure that both the ID (SGD systematic name) and Standard Names were included in each expression table and correct | ||
| + | |||
| + | {{template:cdomin12}} | ||
| + | {{jcowan4}} | ||
| + | [[category:Skinny Genes]] | ||
| + | [[category:Group Projects]] | ||
| + | |||
| + | ==Acknowledgments== | ||
| + | 1. I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment. | ||
| + | |||
| + | 2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source." | ||
| + | [[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 14:00, 25 November 2019 (PST) | ||
| + | |||
| + | ==References== | ||
| + | *Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13 | ||
Latest revision as of 15:45, 3 December 2019
Contents
Datas and Files
Electronic Lab Notebook
Milestone 1
- Annotated Bib completed for Tuesday due date individual journals according to Week 11/12 guidelines
Milestone 2
- Created presentation about the article
- We divided up the work into sections and each focused on our assigned task (each was designated a slide(s) and figure(s))
- Also, worked on annotated bibliography
Milestone 3
- deleted Gweight and Eweight since not conducive to our dataset
- changed "YORF" to "ID" and "Name" to "Standard Name"
- sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
- Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together
Milestone 4
- The QAs worked on organizing the layout and naming the standard names and IDs. (Group worked alongside Prof. Dalquist due to complications)
- In essence, we put in a list of genes into the name translator and found ost of the IDs and standard names, but we had blanks for a good amount of genes.
- We used multiple websites which included: "ORF List <-> Gene List", Synergizer, Bioconductor package
- We recently received all the names to move on with our work.
- We spoke with other groups to ensure that column headers were consistent with how other groups structured the data.
- Deleted duplicate data under alias names
- Filled in missing gaps for names
Milestone 5
Problems
- Data set had duplicate data as well as alias for the duplicate data
- Many IDs/Standard names still were missing
- Manual input was needed to resolve (along with Prof. Dalquist)
Data was no fully complete and research and conversion was needed to move the database project along
Milestone 6
- made sure that all of the rows of data were imported into the database for the expression table
- made sure that both the ID (SGD systematic name) and Standard Names were included in each expression table and correct
Misc. Links
Acknowledgments
1. I worked with User:ymesfin, User:Jcowan4, User:msamdars, and User:dramir36 for this assignment.
2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Cdomin12 (talk) 14:00, 25 November 2019 (PST)
References
- Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
