Electronic notebook: sinorhizobium meliloti

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

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 all the files to the wiki at the team page

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.