Changes between Version 12 and Version 13 of SOPs/go_annotation

Timestamp:

09/28/20 09:04:08 (4 years ago)

Author:

ibarrasa

Comment:

--

SOPs/go_annotation

@@ -13 +13 @@
 [[http://www.broadinstitute.org/gsea/index.jsp|Broad GSEA]]
 
-[[http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page | GSEA Wiki]]
+[[https://www.gsea-msigdb.org/gsea/login.jsp|Download the GSEA software and additional resources to analyze, annotate and interpret enrichment results.]]
+
+[[https://www.gsea-msigdb.org/gsea/msigdb/index.jsp|Explore the Molecular Signatures Database (MSigDB), ]]a collection of annotated gene sets for use with GSEA software.
+
+[[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page | GSEA and MSigDB documentation]]
+
+[[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA | Guidelines for using RNA-seq datasets with GSEA]]
   
    ==== Ranked List ====
-   1. Create a two column file with gene names as first column and numeric values for second column (eg. weight, p-value, etc), does not need to be sorted.
+   1. Create a two column file with gene names as first column and numeric values for second column (eg. log FC), does not need to be sorted and it should have extension ".rnk". 
      * Assigning weights: There is no standard way to assign weights, however, it should reflect some logical order.  GSEA uses the correlation between expression and phenotype to assign weights, if the list is not pre-ordered or ranked.  A similar scheme can be used to rank genes by log2 ratio, t-statistic, or a scoring scheme that takes into account both log ratio and p-value.
      * If a gene list is not unique, duplicate genes can be given a //shared// weight, for eg. if a gene occurs four times in the list it is given a weight of 0.25, if it is unique a weight of 1 is given.
@@ -30 +36 @@
 GSEA will rank the genes
 
-  1.  Create necessary files in correct format for expression, phenotype and chip annotation (see GSEA wiki)
+  1.  Create necessary files in correct format for expression, phenotype and chip annotation ([[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA | see GSEA wiki]])
   1.  Use MSigDB for gene sets or create custom gene sets in correct format
   1.  Run GSEA, use default options to start