Miles Malefyt deliverables

Statement of work

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

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

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