Difference between revisions of "Vkuehn Week 8"

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==='''Electronic Lab Notebook'''===
 
==='''Electronic Lab Notebook'''===
−
'''10.10.2013'''
+
''''10.10.2013''''
 
#Data accessed from  
 
#Data accessed from  
 
uploaded txt file and excel file:
 
uploaded txt file and excel file:
 
:[[Media:VK_Merrell_Compiled_Raw_Data_Vibrio.xls| Merrell Compiled Raw Data VK.xls]]
 
:[[Media:VK_Merrell_Compiled_Raw_Data_Vibrio.xls| Merrell Compiled Raw Data VK.xls]]
 
:[[Media:VK Merrell Compiled Raw Data Vibrio.txt| Merrell Compiled Raw Data VK.txt]]
 
:[[Media:VK Merrell Compiled Raw Data Vibrio.txt| Merrell Compiled Raw Data VK.txt]]
 +
 +
''''10.1.2013''''
 +
Expression dataset manager conveted data resulted in '''.gex file'''
 +
* Generated lines that resulted in error. During the conversion the data for 2010 resulted in '''121 errors'''
 +
* Generated an exception file '''.EX.txt'''
 +
* Used autofilter to determine errors. The errors were all gene not found. This was because it was not updated recently so it is ok to proceed. put in '''EX. xlsx'''
 +
*: My partner had a lot more errors than I did. This is because I was using the newer version while he was using the older dataset. Mine had been updated more recently which is why there were less errors because more of the data matched
 +
*Customize the new Expression Dataset by creating new Color Sets which contain the instructions to GenMAPP for displaying data on MAPPs.
 +
* Input the "Avg_LogFC_all" for the Vibrio dataset created in the excel file
 +
* Create criteria builder for "increased":
 +
*: [Avg_LogFC_all] > 0.25 AND [Pvalue] < 0.05
 +
*: Uploaded color sets
 +
'''MAPPFinder Procedure'''
 +
* Launch MAPPFinder and choose color set and criteria, select gene ontology and p value
 +
* Click "run mappfiner" '''.mapp'''
 +
* Gene Ontology window will open. All of the Gene Ontology terms that have at least 3 genes measured and a p value of less than 0.05 will be highlighted yellow. A term with a p value less than 0.05 is considered a "significant" result. Browse through the tree to see your results. Click on "ranked list"
 +
* Top 10 Gene Ontology terms: '''screenshot'''
 +
* My terms in comparison with my partners are different, this is because he had different gene dataset that was less updated and there were differences in expression because of this.
  
 
{{Template:Vkuehn}}
 
{{Template:Vkuehn}}

Revision as of 17:22, 17 October 2013

Electronic Lab Notebook

'10.10.2013'

  1. Data accessed from

uploaded txt file and excel file:

Merrell Compiled Raw Data VK.xls
Merrell Compiled Raw Data VK.txt

'10.1.2013' Expression dataset manager conveted data resulted in .gex file

  • Generated lines that resulted in error. During the conversion the data for 2010 resulted in 121 errors
  • Generated an exception file .EX.txt
  • Used autofilter to determine errors. The errors were all gene not found. This was because it was not updated recently so it is ok to proceed. put in EX. xlsx
    My partner had a lot more errors than I did. This is because I was using the newer version while he was using the older dataset. Mine had been updated more recently which is why there were less errors because more of the data matched
  • Customize the new Expression Dataset by creating new Color Sets which contain the instructions to GenMAPP for displaying data on MAPPs.
  • Input the "Avg_LogFC_all" for the Vibrio dataset created in the excel file
  • Create criteria builder for "increased":
    [Avg_LogFC_all] > 0.25 AND [Pvalue] < 0.05
    Uploaded color sets

MAPPFinder Procedure

  • Launch MAPPFinder and choose color set and criteria, select gene ontology and p value
  • Click "run mappfiner" .mapp
  • Gene Ontology window will open. All of the Gene Ontology terms that have at least 3 genes measured and a p value of less than 0.05 will be highlighted yellow. A term with a p value less than 0.05 is considered a "significant" result. Browse through the tree to see your results. Click on "ranked list"
  • Top 10 Gene Ontology terms: screenshot
  • My terms in comparison with my partners are different, this is because he had different gene dataset that was less updated and there were differences in expression because of this.
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