Kzebrows Week 15 - Revision history

Kzebrows: /* Electronic Lab Notebook */ update powerpoint link

2015-12-16T00:06:38Z

‎Electronic Lab Notebook: update powerpoint link

Kzebrows: /* Electronic Lab Notebook */ minor edit

2015-12-15T07:32:16Z

‎Electronic Lab Notebook: minor edit

Kzebrows: /* Electronic Lab Notebook */ link to final Power Point

2015-12-15T07:31:32Z

‎Electronic Lab Notebook: link to final Power Point

Kzebrows: /* Electronic Lab Notebook */ edit of electronic lab notebook

2015-12-15T03:50:21Z

‎Electronic Lab Notebook: edit of electronic lab notebook

Kzebrows: /* Electronic Lab Notebook */ edit link

2015-12-15T03:43:39Z

‎Electronic Lab Notebook: edit link

Kzebrows: /* Electronic Lab Notebook */ criterion files tables

2015-12-15T03:43:00Z

‎Electronic Lab Notebook: criterion files tables

Kzebrows: /* Electronic Lab Notebook */ lab notebook edit

2015-12-15T02:36:41Z

‎Electronic Lab Notebook: lab notebook edit

Kzebrows: /* Electronic Lab Notebook */ similarities between RX and RP

2015-12-12T23:39:51Z

‎Electronic Lab Notebook: similarities between RX and RP

Kzebrows: looking at criterion files

2015-12-12T20:14:20Z

looking at criterion files

Kzebrows: /* Electronic Lab Notebook */ adding color sets

2015-12-12T20:09:40Z

‎Electronic Lab Notebook: adding color sets

@@ Line 21: / Line 21: @@
 I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point. I deleted all columns except for GO ID, name of GO term, number changed/present and percentage, number present/number in GO and percentage, regular p value, and adjusted p value.
-[[Media:OTS ShigellaFinalPresentation.pptx | '''Final PowerPoint Presentation''']]
+[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]
 {{Template:Kzebrows}} [[Category: Journal Entry]]

← Older revision		Revision as of 07:32, 15 December 2015
Line 22:		Line 22:

	[[Media:OTS ShigellaFinalPresentation.pptx \| '''Final PowerPoint Presentation''']]		[[Media:OTS ShigellaFinalPresentation.pptx \| '''Final PowerPoint Presentation''']]
−
	{{Template:Kzebrows}} [[Category: Journal Entry]]		{{Template:Kzebrows}} [[Category: Journal Entry]]

← Older revision		Revision as of 07:31, 15 December 2015
Line 20:		Line 20:

	I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx \| here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point. I deleted all columns except for GO ID, name of GO term, number changed/present and percentage, number present/number in GO and percentage, regular p value, and adjusted p value.		I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx \| here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point. I deleted all columns except for GO ID, name of GO term, number changed/present and percentage, number present/number in GO and percentage, regular p value, and adjusted p value.
		+
		+	[[Media:OTS ShigellaFinalPresentation.pptx \| '''Final PowerPoint Presentation''']]

	{{Template:Kzebrows}} [[Category: Journal Entry]]		{{Template:Kzebrows}} [[Category: Journal Entry]]

@@ Line 19: / Line 19: @@
 Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.
-I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point.
+I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point. I deleted all columns except for GO ID, name of GO term, number changed/present and percentage, number present/number in GO and percentage, regular p value, and adjusted p value.
-−
 {{Template:Kzebrows}} [[Category: Journal Entry]]

@@ Line 19: / Line 19: @@
 Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.
-I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point.
+I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point.
 {{Template:Kzebrows}} [[Category: Journal Entry]]

← Older revision		Revision as of 03:43, 15 December 2015
Line 18:		Line 18:

	Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.		Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.
		+
		+	I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[[Media:Filtered MAPPFinder Results.xlsx \| here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point.
		+

	{{Template:Kzebrows}} [[Category: Journal Entry]]		{{Template:Kzebrows}} [[Category: Journal Entry]]

@@ Line 10: / Line 10: @@
 We decided to look at the criterion files for RX and RP -0pt5-10 and RX and RP -1-60. These were the samples at the smallest and largest time points at both concentrations, and by looking at the files and filtering them by the above criteria we were able to find some similarities:
-*RX and RP 0pt5-10 Increased: Metabolic processes
+*RX and RP 0pt5-10 gene expression significantly increased: metabolic processes
-*RX and RP 0pt5-10 Decreased: Ribosome
+*RX and RP 0pt5-10 gene expression significantly decreased: ribosome
-*RX and RP 1-60 Increased: Flagellum
+*RX and RP 1-60 gene expression significantly increased: flagellar production
-*RX and RP 1-60 Decreased: Metabolic processes
+*RX and RP 1-60 gene expression significantly decreased: metabolic processes
 Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files | OTS Files]] page under GenMAPP User Files.
-Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo.
+Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.
 {{Template:Kzebrows}} [[Category: Journal Entry]]

← Older revision		Revision as of 20:14, 12 December 2015
Line 9:		Line 9:
	**Adjusted P by less than 0.1		**Adjusted P by less than 0.1

		+	We decided to look at the criterion files for RX and RP -0pt5-10 and RX and RP -1-60. These were the samples at the smallest and largest time points at both concentrations, and by looking at the files and filtering them by the above criteria we were able to find some similarities:
		+	*RX and RP 0pt5-10 Increased:
		+	*RX and RP 0pt5-10 Decreased:
		+	*RX and RP 1-60 Increased:
		+	*RX and RP 1-60 Decreased:

	Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files \| OTS Files]] page under GenMAPP User Files.		Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files \| OTS Files]] page under GenMAPP User Files.

← Older revision		Revision as of 20:09, 12 December 2015
Line 9:		Line 9:
	**Adjusted P by less than 0.1		**Adjusted P by less than 0.1

		+
		+	Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files \| OTS Files]] page under GenMAPP User Files.
		+
		+	Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo.

	{{Template:Kzebrows}} [[Category: Journal Entry]]		{{Template:Kzebrows}} [[Category: Journal Entry]]