Difference between revisions of "Electronic notebook: sinorhizobium meliloti"
From LMU BioDB 2013
(→Week 13) |
|||
| Line 35: | Line 35: | ||
*it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP | *it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP | ||
*ran the first integration of the data and came up with 5535 errors which is roughly half of the overall genes we loaded. | *ran the first integration of the data and came up with 5535 errors which is roughly half of the overall genes we loaded. | ||
| + | |||
| + | ==Reflection on the Process== | ||
| + | '''What did you learn?''' | ||
| + | *'''With your head?''' | ||
| + | *'''With you Heart''' | ||
| + | *'''with your Hands? (technical skills)''' | ||
| + | '''What lesson will you take away from this project that you will still use a year from now?''' | ||
Revision as of 00:05, 14 December 2013
Contents |
Week 12
- Read the paper on the salinity and sucrose stress on gene expression
- Sorted the raw data into an XML file
- started to compile the raw data
- downloaded all raw data and sorted through the information needed
- used the cys5 and cys3 fold change as well as all the IDs
- Uploaded 300 NaCl compiled data set
Week 13
- I continued to sort the raw data and began to process the data in an xls file
- this was a very repetitive part because it involved a lot of replications for each time set
- finished my compiled raw data and processed raw data, as well as the data ready for GenMAPP
- Made individual LOG fold change ratios for each time point replicate then averaged all of the LOG fold change ratios for each of the time points
- preformed a Tstat test
- Preformed a Pvalue test
- added a row of N next to the gene ID name in the forGenMAPP tab
- uploaded Processed Data
- NOTE:the GenMAPP version of the tab is labeled Complete Processed data_MPM and not forGenMAPP
week 15
- I worked on some of the mistakes that I had made in my prior data sets
- removed AVG_LOGFC_ALL row
- added individual Pvalues and TSTAT for each individual replicate of the experiment instead of one Tstat and P value for the whole experiment
- sanity check concluded the number of genes significantly changed at each time point
- T15- 5520
- T30- 7484
- T60- 6711
- T240- 5901
- Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
- uploaded XLS Version and TXT version, USE THIS
- had to change names of the columns in order to correctly upload to GenMAPP
- system code column was renamed
- Gene ID column was renamed to ID on the Programmers computer to resolve some issues
- it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP
- ran the first integration of the data and came up with 5535 errors which is roughly half of the overall genes we loaded.
Reflection on the Process
What did you learn?
- With your head?
- With you Heart
- with your Hands? (technical skills)
What lesson will you take away from this project that you will still use a year from now?
