Jwoodlee Week 9 - Revision history

Jwoodlee: /* Creating an Expression Dataset in the Expression Dataset Manager, Coloring a MAPP with expression data, and Running MAPPFinder */ added screenshot

2015-11-04T04:34:55Z

‎Creating an Expression Dataset in the Expression Dataset Manager, Coloring a MAPP with expression data, and Running MAPPFinder: added screenshot

Jwoodlee: Not under construction anymore

2015-11-04T04:32:14Z

Not under construction anymore

Jwoodlee: /* Compare Gene Database to Outside Resource */ deleted, not needed

2015-11-04T04:31:03Z

‎Compare Gene Database to Outside Resource: deleted, not needed

Jwoodlee: /* Creating an Expression Dataset in the Expression Dataset Manager, Coloring a MAPP with expression data, and Running MAPPFinder */ added answers

2015-11-04T04:26:45Z

‎Creating an Expression Dataset in the Expression Dataset Manager, Coloring a MAPP with expression data, and Running MAPPFinder: added answers

Jwoodlee: /* .gdb Use in GenMAPP */ edited format

2015-11-04T04:14:54Z

‎.gdb Use in GenMAPP: edited format

← Older revision		Revision as of 04:34, 4 November 2015
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	* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?		* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?
	**5221 IDs were imported, with 121 Exceptions, the error codes were the same as last week: "Gene not found in OrderedLocusNames or any related system." VC2209 was one of the gene IDs that threw an exception. This gene is not in the OrderedLocusNames in the .gdb we created, this is reason to believe that they were not originally present in the Uniprot XML file.		**5221 IDs were imported, with 121 Exceptions, the error codes were the same as last week: "Gene not found in OrderedLocusNames or any related system." VC2209 was one of the gene IDs that threw an exception. This gene is not in the OrderedLocusNames in the .gdb we created, this is reason to believe that they were not originally present in the Uniprot XML file.
		+
		+	[[Image:MAPPFinder2015DBResultsJAW.png]]

← Older revision		Revision as of 04:32, 4 November 2015
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−	~~13-Oct-2015 07:31 5.0M date and time of v cholerae download from GenMAPP builder page~~
−
−
−	~~{{Under Construction}}~~
−
−
	==Export Information==		==Export Information==

← Older revision		Revision as of 04:31, 4 November 2015
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	**5221 IDs were imported, with 121 Exceptions, the error codes were the same as last week: "Gene not found in OrderedLocusNames or any related system." VC2209 was one of the gene IDs that threw an exception. This gene is not in the OrderedLocusNames in the .gdb we created, this is reason to believe that they were not originally present in the Uniprot XML file.		**5221 IDs were imported, with 121 Exceptions, the error codes were the same as last week: "Gene not found in OrderedLocusNames or any related system." VC2209 was one of the gene IDs that threw an exception. This gene is not in the OrderedLocusNames in the .gdb we created, this is reason to believe that they were not originally present in the Uniprot XML file.

−	~~== Compare Gene Database to Outside Resource==~~

−	The OrderedLocusNames IDs in the exported Gene Database are derived from the UniProt XML. It is a good idea to check your list of OrderedLocusNames IDs to see how complete it is using the original source of the data (the sequencing organization, the MOD, etc.) Because UniProt is a protein database, it does not reference any non-protein genome features such as genes that code for functional RNAs, centromeres, telomeres, etc.
−
−	~~Note:~~


	{{Template: Jwoodlee}}		{{Template: Jwoodlee}}

@@ Line 145: / Line 145: @@
 * How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset.  Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?
-**5221 IDs were imported, with 121 Exceptions, the error codes were the same as last week: "Gene not found in OrderedLocusNames or any related system."
+**5221 IDs were imported, with 121 Exceptions, the error codes were the same as last week: "Gene not found in OrderedLocusNames or any related system."  VC2209 was one of the gene IDs that threw an exception.  This gene is not in the OrderedLocusNames in the .gdb we created, this is reason to believe that they were not originally present in the Uniprot XML file.
 == Compare Gene Database to Outside Resource==

@@ Line 135: / Line 135: @@
 Note:
-===Creating an Expression Dataset in the Expression Dataset Manager===
+===Creating an Expression Dataset in the Expression Dataset Manager, Coloring a MAPP with expression data, and Running MAPPFinder===
 I selected the Data menu from the main Drafting Board window and chose Expression Dataset Manager from the drop-down list.
@@ Line 146: / Line 146: @@
 * How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset.  Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?
 **5221 IDs were imported, with 121 Exceptions, the error codes were the same as last week: "Gene not found in OrderedLocusNames or any related system."
 == Compare Gene Database to Outside Resource==