Recent changes to Home

WikiPage Home modified by

Tue, 09 Aug 2011 17:43:23 -0000

--- v2 
+++ v3 
@@ -1,33 +1,0 @@
-Preconditions:
-
-• Cluster.rootDir should be adjusted to fit client root directory (.../Gene Expression Analysis)
-• Java source should be compiled (into .class files) and left in .../tcgaheatsurvival/bin
-.../Gene Expression Analysis should contain .../.../Glioblastoma multiforme and .../.../Ovarian serous cystadenocarcinoma, as well as directories for other cancers to be considered
-• Cancer-specific directories should contain .../Expression-miRNA/.../.../* containing raw miRNA expression data (each file should contain data for a single patient-sample
-• Cancer-specific directories should contain .../clinical/Clinical/.../* containing raw clinical data
-• miRNA expression data for matched and unmatched controls should be left in the cancer-specific directory within .../matched control and .../unmatched control respectively
-
-Heat Mapping
-
-This part of the script automates the formatting of miRNA expression data downloaded from TCGA (Cancer Genome Atlas). Output can be fed into Cluster 3.0. Cluster output can then be fed into Java TreeView and processed into a heat map. The un-scripted/ manual steps to be followed are included in the Cluster 3.0 and Java TreeView manuals (available online and with software download).
-
-Open Terminal. Enter the following commands (replacing cancer-specific terms and root directories as needed):
-
-• cd .../tcgaheatsurvival/bin
-• java -Xmx2000m Cluster Ovarian serous carcinoma After each command, hit Enter and wait for process to end. Feedback (progress) may be provided. .../backend and .../heat maps (within cancer-specific directory) are usually used to contain intermediate/image files
-
-Survival Analysis
-
-This part of the script automates the generation and formatting of survival analysis data. There are 3 main phases in this process:
-
-1. Processing of clinical data 
-2. Processing of miRNA expression data 3. Generation of survival analysis data
-
-Open Terminal. Enter the following commands (replacing cancer-specific terms and root directories as needed):
-
-1. cd .../tcgaheatsurvival/bin 
-2. java -Xmx2000m Clinical Ovarian serous carcinoma OV 
-3. java -Xmx2000m ExpressionDataFilter Ovarian serous carcinoma 
-4. java -Xmx2000m GroupData Ovarian serous carcinoma OV
-
-After entering each command, hit Enter and wait for process to end. Feedback (progress) may be provided.

WikiPage Home modified by

Tue, 09 Aug 2011 17:28:57 -0000

--- v1 
+++ v2 
@@ -1,5 +1,33 @@
-Welcome to your wiki!
-
-This is the default page, edit it as you see fit. To add a page simply reference it within brackets, e.g.: [SamplePage].
-
-The wiki uses [Markdown](/p/tcganalysis/wiki/markdown_syntax/) syntax.
+Preconditions:
+
+• Cluster.rootDir should be adjusted to fit client root directory (.../Gene Expression Analysis)
+• Java source should be compiled (into .class files) and left in .../tcgaheatsurvival/bin
+.../Gene Expression Analysis should contain .../.../Glioblastoma multiforme and .../.../Ovarian serous cystadenocarcinoma, as well as directories for other cancers to be considered
+• Cancer-specific directories should contain .../Expression-miRNA/.../.../* containing raw miRNA expression data (each file should contain data for a single patient-sample
+• Cancer-specific directories should contain .../clinical/Clinical/.../* containing raw clinical data
+• miRNA expression data for matched and unmatched controls should be left in the cancer-specific directory within .../matched control and .../unmatched control respectively
+
+Heat Mapping
+
+This part of the script automates the formatting of miRNA expression data downloaded from TCGA (Cancer Genome Atlas). Output can be fed into Cluster 3.0. Cluster output can then be fed into Java TreeView and processed into a heat map. The un-scripted/ manual steps to be followed are included in the Cluster 3.0 and Java TreeView manuals (available online and with software download).
+
+Open Terminal. Enter the following commands (replacing cancer-specific terms and root directories as needed):
+
+• cd .../tcgaheatsurvival/bin
+• java -Xmx2000m Cluster Ovarian serous carcinoma After each command, hit Enter and wait for process to end. Feedback (progress) may be provided. .../backend and .../heat maps (within cancer-specific directory) are usually used to contain intermediate/image files
+
+Survival Analysis
+
+This part of the script automates the generation and formatting of survival analysis data. There are 3 main phases in this process:
+
+1. Processing of clinical data 
+2. Processing of miRNA expression data 3. Generation of survival analysis data
+
+Open Terminal. Enter the following commands (replacing cancer-specific terms and root directories as needed):
+
+1. cd .../tcgaheatsurvival/bin 
+2. java -Xmx2000m Clinical Ovarian serous carcinoma OV 
+3. java -Xmx2000m ExpressionDataFilter Ovarian serous carcinoma 
+4. java -Xmx2000m GroupData Ovarian serous carcinoma OV
+
+After entering each command, hit Enter and wait for process to end. Feedback (progress) may be provided.

WikiPage Home modified by

Tue, 09 Aug 2011 17:22:18 -0000

Welcome to your wiki! This is the default page, edit it as you see fit. To add a page simply reference it within brackets, e.g.: [SamplePage]. The wiki uses [Markdown](/p/tcganalysis/wiki/markdown_syntax/) syntax.