Difference between revisions of "Miles Malefyt deliverables"
From LMU BioDB 2013
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==Statement of work== | ==Statement of work== | ||
| + | ==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 [[Media:Team_Name_NaCl_compiled_raw_Data.xls|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 [[Media:Complete_processed_Data.xls|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 [[Media:Complete_processed_Data_MPM.xls|XLS Version]] and [[Media:Complete_processed_Data_MPM.txt|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. | ||
| + | *loaded genMAPP and Mappfinder results | ||
| + | *analyzed the Gene Ontology report | ||
| + | **found a specific metabolic pathway that was pertinent to the treatment of NaCl | ||
Revision as of 21:52, 13 December 2013
Contents |
Statement of work
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.
- loaded genMAPP and Mappfinder results
- analyzed the Gene Ontology report
- found a specific metabolic pathway that was pertinent to the treatment of NaCl
