Difference between revisions of "GenMAPP User"
From LMU BioDB 2013
Kdahlquist (Talk | contribs) (added category for group projects) |
Kdahlquist (Talk | contribs) (→Milestone 1: note about citation and copyright) |
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==== Milestone 1 ==== | ==== Milestone 1 ==== | ||
# Find and acquire the microarray paper for your team (done [[Week 10]]). | # Find and acquire the microarray paper for your team (done [[Week 10]]). | ||
| + | #* Provide the proper bibliographic reference for your paper | ||
#* Link to the online version of the paper on the journal web site | #* Link to the online version of the paper on the journal web site | ||
| − | #* Upload the pdf version of the paper to the wiki | + | #* Upload the pdf version of the paper to the wiki ''(if no copyright restrictions)'' |
# Download microarray data in it's "rawest" form that you can find. (Consult with Dr. Dahlquist about this.) | # Download microarray data in it's "rawest" form that you can find. (Consult with Dr. Dahlquist about this.) | ||
# Verify that the gene IDs in the microarray data match the chosen species and '''''strain''''' that is being used to create the .gdb. | # Verify that the gene IDs in the microarray data match the chosen species and '''''strain''''' that is being used to create the .gdb. | ||
Revision as of 19:42, 18 October 2013
Contents |
Guild Members
- To be determined.
Milestones
The milestones do not necessarily correspond to particular weeks, instead they are sets of tasks grouped together.
Milestone 1
- Find and acquire the microarray paper for your team (done Week 10).
- Provide the proper bibliographic reference for your paper
- Link to the online version of the paper on the journal web site
- Upload the pdf version of the paper to the wiki (if no copyright restrictions)
- Download microarray data in it's "rawest" form that you can find. (Consult with Dr. Dahlquist about this.)
- Verify that the gene IDs in the microarray data match the chosen species and strain that is being used to create the .gdb.
- This last task needs to be done in conjunction with the Quality Assurance person and Coder.
- File management: on your team's home page
- Link to the source of the microarray data
- Upload the microarray data files to the wiki
Milestone 2
- Read the microarray paper to understand the experiment.
- Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.
- Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.
- Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.
- Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
Future Milestones
- Perform the statistical analysis in Excel
- Format the gene expression data for import into GenMAPP.
- Import data into GenMAPP, create ColorSets, and run MAPPFinder.
- Document and take notes on test runs with GenMAPP.
- Use the EX.txt file to help the Coders/ID Minders to validate the .gdb
- Do a journal club outline of the paper so that you can use it in the Discussion section of your group report.
- Create a .mapp file showing one pathway that is changed in your data.
