Electronic notebook: sinorhizobium meliloti - Revision history

Mmalefyt: /* Reflection on the Process */

2013-12-14T00:15:04Z

‎Reflection on the Process

2013-12-14T00:05:56Z

2013-12-05T18:03:37Z

‎Week 13

2013-12-05T18:00:58Z

‎Week 13

2013-12-05T17:59:58Z

‎Week 12

2013-12-05T17:58:51Z

‎week 15

2013-12-05T17:57:44Z

‎week 15

2013-12-05T17:47:32Z

‎Week 12

2013-12-05T17:46:00Z

‎week 15

2013-12-03T18:33:25Z

‎Week 12

@@ Line 39: / Line 39: @@
 '''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?'''

← Older revision		Revision as of 00:05, 14 December 2013
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?'''

@@ Line 16: / Line 16: @@
 *added a row of N next to the gene ID name in the forGenMAPP tab
 *uploaded [[Media:Complete_processed_Data.xls|Processed Data]]
 ==week 15==

@@ Line 15: / Line 15: @@
 *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
+*uploaded [[Media:Complete_processed_Data.xls|Processed Data]]
 ==week 15==

@@ Line 5: / Line 5: @@
 **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==

@@ Line 26: / Line 26: @@
 **T240- 5901
 *Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
-*uploaded
+*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

@@ Line 3: / Line 3: @@
 *Sorted the raw data into an XML file
 *started to compile the raw data
 ==Week 13==

← Older revision		Revision as of 17:46, 5 December 2013
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	**T240- 5901		**T240- 5901
	*Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data		*Removed all of the #DIV/0! from the data that was transferred over to the GenMapp data
		+	*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
		+	*it appears that there is something wrong with the actual gene IDs that is not compatible with GenMAPP

← Older revision		Revision as of 18:33, 3 December 2013
Line 2:		Line 2:
	*Read the paper on the salinity and sucrose stress on gene expression		*Read the paper on the salinity and sucrose stress on gene expression
	*Sorted the raw data into an XML file		*Sorted the raw data into an XML file
		+	*started to compile the raw data
		+
		+	==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