← Older revision

Revision as of 03:00, 13 December 2013

Line 78:

Note:

−

==TallyEngine==

+

===TallyEngine===

[[Image:Leishmania TallyResults 05122013.PNG]]

−

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

+

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

[[Image:Leishmania Match Results 05122013 2.PNG]]

Line 89:

:*We found 8353, we are missing 2 ORFs, but cannot reach the stragglers via coding.

−

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

+

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

:'''select value from genenametype where type='ORF' and not value ~ 'L[Mm][Jj]F([\. _]|)[0-9][0-9][\. _][0-9][0-9][0-9][0-9]';'''

:[[Image:Leishmania postgres.PNG]]

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:8350 that match original pattern, 5 stragglers. There is an inconsistancy in patterns where some have underscores, some have periods, some have spaces. We were unable to capture all IDs at once.

−

==OriginalRowCounts Comparison==

+

===OriginalRowCounts Comparison===

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Line 105:

Note: [[Image:Leishmania OrginialRowCounts 07122013.PNG]]

−

==Visual Inspection==

+

===Visual Inspection===

Perform visual inspection of individual tables to see if there are any problems.

Line 117:

*All IDs appear to take the correct form for that type of ID.

−

==.gdb Use in GenMAPP==

+

===.gdb Use in GenMAPP===

Note: Most GDB use in GenMAPP is profiled on the GenMAPP users page

@@ Line 117: / Line 117: @@
 *All IDs appear to take the correct form for that type of ID.
-==.gdb Use in GenMAPP==
+=='''.gdb Use in GenMAPP'''==
 Note: Most GDB use in GenMAPP is profiled on the GenMAPP users page
@@ Line 127: / Line 127: @@
 Note: All IDs seem to be present.
-==Creating an Expression Dataset in the Expression Dataset Manager==
+=='''Creating an Expression Dataset in the Expression Dataset Manager'''==
 * 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?
@@ Line 136: / Line 136: @@
 Note: Coloring successfully yielded graphical depiction of expression data
-==Running MAPPFinder==
+=='''Running MAPPFinder'''==
 Note: See final project deliverables (.mapp)and (.xls)

@@ Line 117: / Line 117: @@
 *All IDs appear to take the correct form for that type of ID.
-===.gdb Use in GenMAPP===
+==.gdb Use in GenMAPP==
 Note: Most GDB use in GenMAPP is profiled on the GenMAPP users page
@@ Line 127: / Line 127: @@
 Note: All IDs seem to be present.
-===Creating an Expression Dataset in the Expression Dataset Manager===
+==Creating an Expression Dataset in the Expression Dataset Manager==
 * 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?
@@ Line 136: / Line 136: @@
 Note: Coloring successfully yielded graphical depiction of expression data
-===Running MAPPFinder===
+==Running MAPPFinder==
 Note: See final project deliverables (.mapp)and (.xls)

Leishmania major - Revision history

Lena at 03:03, 13 December 2013

Lena at 03:02, 13 December 2013

Lena at 03:00, 13 December 2013

@@ Line 78: / Line 78: @@
 Note:
-==TallyEngine==
+===TallyEngine===
 [[Image:Leishmania TallyResults 05122013.PNG]]
-== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==
+===Using XMLPipeDB match to Validate the XML Results from the TallyEngine===
 [[Image:Leishmania Match Results 05122013 2.PNG]]
@@ Line 89: / Line 89: @@
 :*We found 8353, we are missing 2 ORFs, but cannot reach the stragglers via coding.
-== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==
+=== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine===
 :'''select value from genenametype where type='ORF' and not value ~ 'L[Mm][Jj]F([\. _]|)[0-9][0-9][\. _][0-9][0-9][0-9][0-9]';'''
 :[[Image:Leishmania postgres.PNG]]
@@ Line 97: / Line 97: @@
 :8350 that match original pattern, 5 stragglers.  There is an inconsistancy in patterns where some have underscores, some have periods, some have spaces.  We were unable to capture all IDs at once.
-==OriginalRowCounts Comparison==
+===OriginalRowCounts Comparison===
 Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.
@@ Line 105: / Line 105: @@
 Note: [[Image:Leishmania OrginialRowCounts 07122013.PNG]]
-==Visual Inspection==
+===Visual Inspection===
 Perform visual inspection of individual tables to see if there are any problems.
@@ Line 117: / Line 117: @@
 *All IDs appear to take the correct form for that type of ID.
-==.gdb Use in GenMAPP==
+===.gdb Use in GenMAPP===
 Note: Most GDB use in GenMAPP is profiled on the GenMAPP users page