Difference between revisions of "Leishmania major Week 13 Status Report"

Latest revision as of 05:30, 22 November 2013

[edit] Import/Export GenMAPP

Name:Leishmania_major_18112013

[edit] Export Information

Uniprot: 7.42 minutes

File:UniprotXML Leishmania 05112013 Gabe Lena.xml

GO OBO: 5.96 minutes

File:Leishmania 05112013 Gabe Lena.obo-xml.gz

GOA: 0.04 minutes

File:LeishmaniaGOA 19112013 Lena Gabe.goa

[edit] Files

Newly Updates Database:File:Leishmania major 19112013 Dist.zip

Name of .gdb File:Media:LeishmaniaGDB 21112013 Lena Gabe.gdb

Fixed Microarray Data:File:L.majorCompiledRawData C 21112013.txt

[edit] Reflections

[edit] Lena Hunt

1.)We got our database to export into GenMAPP. Originally it was showing a generic database, and it wouldn't recognize the OrderedLocusNames. We fixed it in Eclipse and uploaded it to the homepage. We then successfully got GenMAPP to recognize our database. We also updated our microarray data so that the gene IDs did not have extra numbers (we used the : as a separator.) We then went through and changed all the "Error" messages with a 0 so as not to confuse GenMAPP.

2.)We managed to work through all the things that didn't work this week. At this time we are waiting for the export to complete to test gene database link and microarray data.

3.)Currently we do not have any problems we are aware of, but after a entire work session of working through problems today, I think we are prepared to work through problems that may come up in the next work session.

[edit] Gabriel Leis

1. What worked?

   As a team we accomplished almost all goals for the week. Successful organization allowed team members from various "guilds" receive the information needed to accomplish various tasks.

2. What didn't work?

   Initial screening of new database yielded an error but the error appears to have been fixed.

3. What will I do next to fix what didn't work?

   Continue with exported .gdb to identify necessary edits in the code for customizations to Leishmania major database

Gleis (talk) 21:30, 21 November 2013 (PST)

[edit] Kevin McGee

1. We were able to successfully analyze our GenMAPP data to prepare it for import to GenMAPP
2. It was hard to relate some of the commands from VC to our data set because there were some major differences in the data that we had.
3. Trying to fully understand all the columns and the cells will help us understand what is different from our data compared to VC and therefore how to handle the data differently

Kevinmcgee (talk) 11:08, 21 November 2013 (PST)

[edit] Viktoria Kuehn

1. What worked?

   We got all of the data ready for import to GenMAPP

2. What didn't work?

   Some of the data had errors instead of values

3. What will I do next to fix what didn't work?

   We already fixed this by making those blank and not using them in the statistical analysis

[edit] GenMAPP Data

1. Centered and Scaled the Microarray data
2. Found the Average Fold Change
3. Statistical Analysis: Found P-value and T-test
4. Formatted to be compatible with GenMAPP
5. Saved for GenMAPP as a txt file

   For more detailed procedure info see Vkuehn Week 13 for major or, for infantum see Kevinmcgee Week 13

   The files can be found under Leishmania major in the File Updates section