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Revision as of 10:14, 27 October 2015

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'' '''Checkpoint: There were 772 errors in the 2009 data file. The gex file is located [[Media:Merrell Compiled Raw Data Vibrio TR 20151019.gex | here]]. The EX.txt file can be found [[Media:Merrell Compiled Raw Data Vibrio TR 20151019.EX.txt | here]].''' ''

'' '''Checkpoint: There were 772 errors in the 2009 data file. The gex file is located [[Media:Merrell Compiled Raw Data Vibrio TR 20151019.gex | here]]. The EX.txt file can be found [[Media:Merrell Compiled Raw Data Vibrio TR 20151019.EX.txt | here]].''' ''

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[[Image:GenMAPP errors.jpg]]

=== GenMAPP Expression Dataset Manager Procedure ===

=== GenMAPP Expression Dataset Manager Procedure ===

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* Then, I allowed the Expression Dataset Manager to convert my data.

* Then, I allowed the Expression Dataset Manager to convert my data.

** This probably only took a couple of seconds to 1 minute. When the process completed, the converted dataset was active in the Expression Dataset Manager window and the file saved in the same folder the raw data file was in, named the same except with a .gex extension; for example, MyExperiment.gex.

** This probably only took a couple of seconds to 1 minute. When the process completed, the converted dataset was active in the Expression Dataset Manager window and the file saved in the same folder the raw data file was in, named the same except with a .gex extension; for example, MyExperiment.gex.

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** Here is an image of what the loading screen should look like:

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** [[Media:GenMAPP loading.jpg]]

** A message appeared saying that the Expression Dataset Manager could not convert one or more lines of data. Lines that generated an error during the conversion of a raw data file were not added to the Expression Dataset. Instead, an exception file was created. The exception file is given the same name as my raw data file with .EX before the extension (e.g., MyExperiment.EX.txt). The exception file contained all of my raw data, with the addition of a column named ~Error~. This column contained either error messages or, if the program found no errors, a single space character.

** A message appeared saying that the Expression Dataset Manager could not convert one or more lines of data. Lines that generated an error during the conversion of a raw data file were not added to the Expression Dataset. Instead, an exception file was created. The exception file is given the same name as my raw data file with .EX before the extension (e.g., MyExperiment.EX.txt). The exception file contained all of my raw data, with the addition of a column named ~Error~. This column contained either error messages or, if the program found no errors, a single space character.

*** '''The number of errors came out to be 772. After opening the EX txt file, I discovered that the errors were caused by "Gene not found in OrderedLocusNames or any related system." for all 772 errors that came up when the was processed.'''

*** '''The number of errors came out to be 772. After opening the EX txt file, I discovered that the errors were caused by "Gene not found in OrderedLocusNames or any related system." for all 772 errors that came up when the was processed.'''

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* I saved the entire Expression Dataset by selecting Save from the Expression Dataset menu.

* I saved the entire Expression Dataset by selecting Save from the Expression Dataset menu.

* I then exited the Expression Dataset Manager to view the Color Sets on a MAPP by clicking the close box in the upper right hand corner of the window.

* I then exited the Expression Dataset Manager to view the Color Sets on a MAPP by clicking the close box in the upper right hand corner of the window.

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* This is the result of entering the criterion:

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[[Media:GenMAPP creating criterion.jpg]]

=== MAPPFinder Procedure ===

=== MAPPFinder Procedure ===

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* I made sure that the Gene Database for the correct species is loaded.  The name of the Gene Database appears at the bottom of the window.  If this is not the right one, go to File > Choose Gene Database and choose the correct one.  (The Gene Databases are stored in the folder C:\GenMAPP 2 Data\Gene Databases\.)

* I made sure that the Gene Database for the correct species is loaded.  The name of the Gene Database appears at the bottom of the window.  If this is not the right one, go to File > Choose Gene Database and choose the correct one.  (The Gene Databases are stored in the folder C:\GenMAPP 2 Data\Gene Databases\.)

* I clicked on the button "Calculate New Results".

* I clicked on the button "Calculate New Results".

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* [[Media:MAPPFinder menu.jpg]]

* I clicked on "Find File".

* I clicked on "Find File".

** MAPPFinder found it for me already.

** MAPPFinder found it for me already.

* I chose the Color Set and Criteria with which to filter the data and clicked on the "Decreased" criteria in the right-hand box.

* I chose the Color Set and Criteria with which to filter the data and clicked on the "Decreased" criteria in the right-hand box.

* I checked the boxes next to "Gene Ontology" and "p value".

* I checked the boxes next to "Gene Ontology" and "p value".

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** [[Media:MAPPFinder calculate results window.jpg]]

* I then clicked the "Browse" button and created a meaningful filename for my results.

* I then clicked the "Browse" button and created a meaningful filename for my results.

* I also clicked "Run MAPPFinder".  The analysis took only a couple of minutes.

* I also clicked "Run MAPPFinder".  The analysis took only a couple of minutes.

Troque Week 8 - Revision history

Troque: Changed "Media" into "Image"

Troque: Linking images to this page