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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.

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 or install multiple versions of R?

Better not for upgrading. Installing multiple versions of R is OK provided you know some details described below.

Each version of BRB-ArrayTools has been tested with a certain version of R. So there maybe a compatibility problem with certain functions used in the code if you decide to upgrade R.

• BRB-ArrayTools (up to v4.2.1) requires StatconnDCOM which means the following conditions have to be satisfied:
  • R needs to registered in the Windows's registry (it should be done if you accept all default options when R was installed).
  • The R package 'rscproxy' has to be installed under the library folder the registered R. It cannot be installed under user's Document's folder as other R's packages.

• BRB-ArrayTools (from v4.3.0) requires Rserve package. That means
  • Rserve has to be installed. It does not have to be installed under R\library folder.
  • Rserve.exe from R\librar\Rserve\inst\i386 and x64 subfolder has to be copied to R\bin\i386 and R\bin\x64 folder.

If you need to use the latest version of R for your own analysis, you can still make it. First, install the latest version of R as usual. Then install again the full-version of BRB-ArrayTools. This will possibly install another version of R and register it in the Windows's registry for BRB-ArrayTools to use. Now you can enjoy both versions of R as you want. The idea is when you install R, it will by default register R, but this behavior can break the setting for R to be used by BRB-ArrayTools. Once you install BRB-ArrayTools, it will install an R it needs and not erase any other versions of R you already have.

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.

Citing

http://www.citeulike.org/search/all?q=arraytools

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.