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| '''Your friend to BRB-ArrayTools.'''
| | Shortcuts to some pages that may be useful to you! |
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| == Features == | | {| |
| | |style="width: 5%; border-width: 0px;"|[[File:Dna microarray45.png|link=Arraytools|BRB-ArrayTools]]||style="width: 20%; border-width: 0px;"|[[Arraytools|BRB-ArrayTools]]||style="width: 5%; border-width: 0px;"|[[File:linux48.png|link=Linux|Linux]]||style="width: 20%; border-width: 0px;"|[[Linux|Linux]]||style="width: 5%; border-width: 0px;"|[[File:R_logo48.png|link=R|R]]||style="width: 20%; border-width: 0px;"|[[R|R]] |
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| | || [[File:tai-chi48.png|link=Tai_Chi|Tai Chi]] || [[Tai_Chi|Tai Chi]] || [[File:heart48.png|link=Health|Health]] || [[Health|Health]] || [[File:raspberry48.png|link=Raspberry|Raspberry Pi]] || [[Raspberry|Raspberry Pi]] |
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| | || [[File:docker48.png|link=Docker|Docker]] |
| | || [[Docker|Docker]] |
| | || [[File:recipe48.png|link=Recipes|Recipes]] |
| | || [[Recipes|Recipes]] |
| | || [[File:statistics48.png|link=Statistics|Statistics]] |
| | || [[Statistics|Statistics]] |
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| | || [[File:ubuntulogo48.png|link=Ubuntu|Ubuntu]] |
| | || [[Ubuntu|Ubuntu]] |
| | || [[File:vblogo48.png|link=Virtualbox|Virtualbox]] |
| | || [[Virtualbox|Virtualbox]] |
| | || [[File:beaglebone48.png|link=Beaglebone|Beaglebone]] |
| | || [[Beaglebone|Beaglebone]] |
| | |} |
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| === Import from multiple data types ===
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| Expression data, Illumina methylation data, Copy number data (CGH-Tools), RNA-Seq count data processed through Galaxy web tool.
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| === Sophisticated statistical analysis tools ===
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| Class comparison for differential expression, class prediction, graphical 2d and 3D interactive plots, gene set analysis, and more.
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| === Comprehensive biological annotations ===
| | MC Li |
| Gene ontology, pathways, protein domain, broad msigdb, lymphoid signatures, experimentally verified transcription factor targets, computationally predicted microRNA targets.
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| == Screenshots ==
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| ==== [[File:BRB_HeatmapDendrogram.png|100px]] Heatmap and dendrogram generated from the Pomeroy sample dataset. ====
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| ==== [[File:BRB_3Dplot.png|100px]] Interactive 3D scatterplot of samples from running the multidimensional scaling analysis on the Pomeroy dataset. ====
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| ==== [[File:BRB_Scatterplot.png|100px]] Interactive 2D scatterplot of samples with gene annotation from a selected gene using right click menu. ====
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| ==== [[File:VolcanoPlot.png|100px]] Interactive volcano plot from the output of running a class comparison tool. ====
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| == FAQs ==
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| === General ===
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| ==== How to install BRB-ArrayTools if you have 64-bit MS-Office? ====
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| There is no difference in terms of the installation.
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| ==== If installation, I can not find the BRB-ArrayTools in Windows > Start > All Programs. ====
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| Check EXCEL.
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| ==== Can I upgrade R or install multiple versions of R? ====
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| Better not for upgrading. Installing multiple versions of R is OK provided you know some details described below.
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| 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.
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| * BRB-ArrayTools (up to v4.2.1) requires StatconnDCOM which means the following conditions have to be satisfied:
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| ** R needs to registered in the Windows's registry (it should be done if you accept all default options when R was installed).
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| ** 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.
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| * BRB-ArrayTools (from v4.3.0) requires Rserve package. That means
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| ** Rserve has to be installed. It does not have to be installed under R\library folder.
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| ** Rserve.exe from R\librar\Rserve\inst\i386 and x64 subfolder has to be copied to R\bin\i386 and R\bin\x64 folder.
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| 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.
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| ==== Rserve ====
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| 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.
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| See my [[Rserve]] wiki page.
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| === Analysis ===
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| ==== Best parameter or analysis to choose ====
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| Ask your local help desk.
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| ==== For affy cel files, GCRMA has a memory problem and MAS5 is way too slow ====
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| 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.
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| == Citing ==
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| * [http://www.citeulike.org/search/all?q=arraytools citeulike]
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| * [http://scholar.google.com/scholar?hl=en&lr=&scoring=r&q=BRB+ArrayTools&as_ylo=1900&btnG=Search google scholar]
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| == Support ==
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| Please provide enough information to us so we can understand the problem.
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| * If a bug report file was generated, be sure to send it to us.
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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.
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| * 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.
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| * 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.
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| === Check BRB-ArrayTools message board [http://linus.nci.nih.gov/cgi-bin/brb/board1.cgi] ===
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