Dwilliams Week 9 assignment - Revision history

Dwilliams: /* Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine */ Added response

2013-10-25T02:20:55Z

‎Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine: Added response

2013-10-25T02:20:17Z

‎Compare Gene Database to Outside Resource

2013-10-25T02:20:01Z

‎.gdb Use in GenMAPP: Added answers

2013-10-25T02:19:03Z

‎Visual Inspection: Added answers

2013-10-25T02:16:44Z

‎OriginalRowCounts Comparison: Added Screenshots

2013-10-25T02:12:02Z

‎Using XMLPipeDB match to Validate the XML Results from the TallyEngine: Added Answers

2013-10-25T02:03:11Z

‎TallyEngine: Added Image

2013-10-25T01:59:33Z

Fixed uploaded file

2013-10-25T01:58:52Z

Added uploaded file

2013-10-25T01:56:34Z

Added Time taken to export

← Older revision		Revision as of 02:20, 25 October 2013
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	[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL \| Follow the instructions on this page to query the PostgreSQL Database.]]		[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL \| Follow the instructions on this page to query the PostgreSQL Database.]]
		+
		+	*Followed SQL queries instructions in order to obtain the required data.

	==OriginalRowCounts Comparison==		==OriginalRowCounts Comparison==

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 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:
+Note: This step could not be done due to an error that was explained in class.
 <!--In this example, this query tells you which IDs are in Riley only:<br>
 select Riley.ID from Riley left outer join Blattner on Riley.ID = Blattner.ID where Blattner.ID is null;-->

@@ Line 73: / Line 73: @@
 ==.gdb Use in GenMAPP==
-Note:
+Note: This step could not be done due to an error that was explained in class.
 ===Putting a gene on the MAPP using the GeneFinder window===
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 * Try a sample ID from each of the gene ID systems. Open the Backpage and see if all of the cross-referenced IDs that are supposed to be there are there.
-Note:
+Note: This step could not be done due to an error that was explained in class.
 ===Creating an Expression Dataset in the Expression Dataset Manager===
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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?
-Note:
+Note: This step could not be done due to an error that was explained in class.
 ===Coloring a MAPP with expression data===
-Note:
+Note: This step could not be done due to an error that was explained in class.
 ===Running MAPPFinder===
-Note:
+Note: This step could not be done due to an error that was explained in class.
 == Compare Gene Database to Outside Resource==

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 * Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
 * Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?
 Note:

← Older revision		Revision as of 02:16, 25 October 2013
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	Copy the OriginalRowCounts table and paste it here:		Copy the OriginalRowCounts table and paste it here:
		+
		+	[[Image:Screen Shot 2013-10-24 at 7.13.32 PM.png\| Column 1]]
		+
		+	[[Image:Screen Shot 2013-10-24 at 7.13.54 PM.png\| Column 2]]

	Note:		Note:

← Older revision		Revision as of 02:12, 25 October 2013
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	Are your results the same as you got for the TallyEngine? Why or why not?		Are your results the same as you got for the TallyEngine? Why or why not?
		+
		+	*No, they are not. At first the total number of unique matches was 2738. This was because the letter A was not accounted for in the VC search.
		+	*After including the A, the total number of unique matches stood at 3831, which did indeed match.

	== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==		== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

← Older revision		Revision as of 02:03, 25 October 2013
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	Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the PostgreSQL databases (or you can upload and link to a screenshot of the results).		Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the PostgreSQL databases (or you can upload and link to a screenshot of the results).
		+
		+	[[Image: Screen_Shot_2013-10-24_at_7.01.11_PM.png\| Screen Shot]]

	== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==		== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

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 Name of .gdb file: Vc-Std_dwilliams-20131022-gmb2b70.gdb
 * Time taken to export .gdb: 90 minutes and 56 seconds.
-* Upload your file and link to it here. [[Media:File:Vc-Std dwilliams-20131022-gmb2b70.gdb| Results]]
+* Upload your file and link to it here. [[Media:Vc-Std dwilliams-20131022-gmb2b70.gdb| Results]]
 Note: Export concluded at 12:10:56 pm