Dear all,1. While using ClueGO in Cytoscape is it possible to load custom background gene list while doing any form of analysis (pathway, biological process etc) using ClueGO analysis.
2. After deriving a network using ClueGO will it be possible to derive (a) p-value and (b) FDR for each node and edges as well as for each gene or compounds that were used to create the network.
3. Will it be possible to get a summary statistics for all nodes, edges and input genes or metabolites associated with the network?
Please let me know.Thanks, Nara
Hi Bernhard,I) Can you please share the documentation on how to create 1) correlation matrices, 2) ttests, 3) visualize the expression data on gene nodes in the network.
II) Also please let me know how to get enrichment analysis stats for Pathway nodes.
Thank you,Nara
From: Bernhard <gabriel...@gmail.com>
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Sunday, 25 February 2018, 22:35
Subject: [cytoscape-helpdesk] Re: 1) Background gene set for ClueGO and 2) summary statistics (p-value and FDR)
Hi Nara,--
On Wednesday, February 14, 2018 at 7:45:06 AM UTC+1, BIOMICS wrote:Dear all,1. While using ClueGO in Cytoscape is it possible to load custom background gene list while doing any form of analysis (pathway, biological process etc) using ClueGO analysis.You can load data sets under CluePedia and make correlation matrices, or ttests, or visualize the expression data on gene nodes in the network.2. After deriving a network using ClueGO will it be possible to derive (a) p-value and (b) FDR for each node and edges as well as for each gene or compounds that were used to create the network.ClueGO only calculates enrichment (fisher's exact test) p-values for the GO / Pathway nodes.3. Will it be possible to get a summary statistics for all nodes, edges and input genes or metabolites associated with the network?What kind of statistics are you thinking on? Normally enrichment analysis stats are only for Pathway nodes.Please let me know.Thanks, NaraBest
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