Recent changes to Data loading

Data loading modified by Keith Ching

Keith Ching — Tue, 01 Mar 2016 17:48:53 -0000

--- v5
+++ v6
@@ -23,5 +23,5 @@
 Mutation formats varied between TCGA releases such that identical, yet unique mutations may be entered. eg. KRAS G12D, p.G12D.  Try to catch these and remove. fixMutations.pl

 EXPRESSION
-Normalized RSEM values from TCGA are log2.  Any zero or negative values are set to 0.01
+Normalized RSEM values from TCGA are converted to log2.  Any zero or negative values are set to 0.01
 Values are stored in the database as integers. ( expression x 1000).  They need to be divided by 1000 after retrieval.

Data loading modified by Keith Ching

Keith Ching — Tue, 01 Mar 2016 17:48:25 -0000

--- v4
+++ v5
@@ -13,3 +13,15 @@
 CNV
 too many fragments is an indication that the SNP6 chip failed.
 remove samples >=3500 segments from the database.
+
+MYSQL
+Data cleaned with cleanDatabase.pl and cleanDatabaseMETA.pl
+Optimized tables to shrink database size after cleaning.
+mysqlcheck -o <db_name> -u <username> -p
+
+MUTATIONS
+Mutation formats varied between TCGA releases such that identical, yet unique mutations may be entered. eg. KRAS G12D, p.G12D.  Try to catch these and remove. fixMutations.pl
+
+EXPRESSION
+Normalized RSEM values from TCGA are log2.  Any zero or negative values are set to 0.01
+Values are stored in the database as integers. ( expression x 1000).  They need to be divided by 1000 after retrieval.

Data loading modified by Keith Ching

Keith Ching — Mon, 30 Nov 2015 21:23:09 -0000

--- v3
+++ v4
@@ -9,3 +9,7 @@

 [RNA-Seq]
+
+CNV
+too many fragments is an indication that the SNP6 chip failed.
+remove samples >=3500 segments from the database.

Data loading modified by Keith Ching

Keith Ching — Mon, 13 Apr 2015 17:47:47 -0000

--- v2
+++ v3
@@ -6,3 +6,6 @@
   2. process files
   3. parse files
   4. load files
+
+
+[RNA-Seq]

Data loading modified by Keith Ching

Keith Ching — Fri, 10 Oct 2014 22:38:22 -0000

--- v1
+++ v2
@@ -0,0 +1,8 @@
+Loading data into CELLX
+
+
+TCGA
+  1. fetch files
+  2. process files
+  3. parse files
+  4. load files

Data loading modified by Keith Ching

Keith Ching — Fri, 10 Oct 2014 22:36:46 -0000