Miles Malefyt deliverables - Revision history

Mmalefyt: /* week 15 */

2013-12-13T23:32:29Z

‎week 15

Mmalefyt: /* week 15 */

2013-12-13T23:05:43Z

‎week 15

Mmalefyt: /* Statement of work */

2013-12-13T21:52:30Z

‎Statement of work

Mmalefyt: Created page with "==Statement of work=="

2013-12-13T21:48:43Z

Created page with "==Statement of work=="

New page

==Statement of work==

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 [[Media:MAPPFinder_results_T15-Criterion_Increased-GO.txt|Increased expression at T15]]
 [[Media:MAPPFinder_results_T15-Criterion_Decreased-GO.txt|Decreased expression at T15]]
 [[Media:MAPPFinder_t60-Criterion_Increased-GO.txt|Increased expression at t60]]
 [[Media:MAPPFinder_t60-Criterion_Decreasaed-GO.txt|Decreased expression at t60]]
 *analyzed the Gene Ontology report
 **found a specific metabolic pathway that was pertinent to the treatment of NaCl

@@ Line 35: / Line 35: @@
 *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

← Older revision		Revision as of 21:52, 13 December 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