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* If the question is like 'what method or parameters should be choose to run my analysis', please consult other experienced people near you. | * If the question is like 'what method or parameters should be choose to run my analysis', please consult other experienced people near you. | ||
* Since the software depends on a couple factors like Windows operation system, MS-Office, R. Please provide us more detailed information about the software background including BRB-ArrayTools. | * Since the software depends on a couple factors like Windows operation system, MS-Office, R. Please provide us more detailed information about the software background including BRB-ArrayTools. | ||
* When sending screenshots to us, please provide all error screenshots. If you only provide any random of them, it will create a misleading to us. | |||
=== Check BRB-ArrayTools message board [http://linus.nci.nih.gov/cgi-bin/brb/board1.cgi] === | === Check BRB-ArrayTools message board [http://linus.nci.nih.gov/cgi-bin/brb/board1.cgi] === | ||
Revision as of 09:18, 24 October 2012
Your friend to BRB-ArrayTools.
Features
Import from multiple data types
Expression data, Illumina methylation data, Copy number data (CGH-Tools), RNA-Seq count data processed through Galaxy web tool.
Sophisticated statistical analysis tools
Class comparison for differential expression, class prediction, graphical 2d and 3d interactive plots, gene set analysis, and more.
Comprehensive biological annotations
Gene ontology, pathways, protein domain, broad msigdb, lymphoid signatures, experimentally verified transcription factor targets, computationally predicted microRNA targets.
Screenshots
Heatmap and dendrogram generated from the Pomeroy sample dataset.
Interactive 3D scatterplot of samples from running the multidimensional scaling analysis on the Pomeroy dataset.
Interactive 2D scatterplot of samples with gene annotation from a selected gene using right click menu.
Interactive volcano plot from the output of running a class comparison tool.
FAQs
General
How to install BRB-ArrayTools if you have 64-bit MS-Office?
There is no difference in terms of the installation.
If installation, I can not find the BRB-ArrayTools in Windows > Start > All Programs.
Check EXCEL.
Can I upgrade R?
Better not.
Can I install multiple versions of R?
Yes.
Rserve
Since version 4.3.0, BRB-ArrayTools started to use Rserve as a media for the communication between R and Excel. When Rserve is required, an R window will be pop up. This R window has a blue icon on the Windows' taskbar. If you accidentally close it, it will be automatically popped up when it is needed.
See my Rserve wiki page.
Analysis
Best parameter or analysis to choose
Ask your local help desk.
For affy cel files, GCRMA has a memory problem and MAS5 is way too slow
It is a known problem. BRB-ArrayTools uses justGCRMA() function in 'gcrma' package for GCRMA option and justMAS() function in 'simpleaffy' package for MAS5 option.
Support
Send an email to [email protected]
Please provide enough information to us so we can understand the problem.
- If a bug report file was generated, be sure to send it to us.
- If the question is like 'what method or parameters should be choose to run my analysis', please consult other experienced people near you.
- Since the software depends on a couple factors like Windows operation system, MS-Office, R. Please provide us more detailed information about the software background including BRB-ArrayTools.
- When sending screenshots to us, please provide all error screenshots. If you only provide any random of them, it will create a misleading to us.