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| '''Your friend to [http://linus.nci.nih.gov/BRB-ArrayTools.html 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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| The right click menu gives an option to highlight up/down-regulated genes, export gene list, copy plot to clipboard, highlight genes in gene set, link genes among plots and change properties of the plot like title, point size, color of points, fold change threshold for up/down regulated genes.
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| ==== [[File:VolcanoPlot.png|100px]] Interactive volcano plot from the output of running a class comparison tool. ====
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| When you move mouse over a gene (point), the gene unique ID and/or symbol will be popped up.
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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. ArrayTools and CGHTools are under the menu of Addon.
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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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| ==== RExcel-statconnDCOM gave an error ====
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| Please upgrade BRB-ArrayTools to v4.3.x where Rserve has replaced statconnDCOM.
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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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| === Importing ===
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| ==== Multiple chips (hgu133a and hgu133b) ====
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| ==== Is my chip recognized by BRB-ArrayTools ====
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| === Annotation ===
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| ==== SOURCE at stanford is down ====
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| During the period of time when SOURCE website is down, our users will not be able to import annotations from SOURCE database. The bioconductor annotation packages will still work for users having Affymetrix or Illumina array data. For non-Affymetrix and non-Illumina chip users who are creating new projects, here are a couple of alternative solutions,
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| * If the user has an existing annotated project with an identical chip type to the project he/she is creating, he/she can import the annotations from the existing project. This can be done by clicking on 'ArrayTools -> Utilities -> Annotate the data -> Import annotations from an existing project';
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| * If the user has an annotation file available, during the process of importing, the user can choose to import annotations from this file. At the step of selecting Gene Identifiers, the user can browse for the Gene Identifiers file and check the option 'Annotate the project with these gene ids, instead of using the data from SOURCE database';
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| * If the user does not have an annotation file, for most commonly used commercial chips, the annotation files can be downloaded from GEO database at NCBI. For instance, the annotation file for the Agilent-014850 Whole Human Genome Microarray chip can be downloaded at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4133 by clicking on the 'Download full table' button. This downloaded annotation file can then be imported into BRB-ArrayTools following step 2).
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| ==== Gene ST array annotation using aroma.affymetrix ====
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| The aroma.affymetrix can handle all single-channel Affymetrix chip types (they have a few multi-channel ones not supported), so my guess is that it is already supported. What's required for nearly all aroma analysis, is to have a CDF annotation file that defines the units and unit groups, e.g. probe sets of transcripts and exons, SNPs and so on.
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| When Affymetrix is not providing a CDF, the challenge is to either find a custom CDF (e.g. BrainArray and GeneAnnot) or to create a one from the other types of annotation data they or Bioconductor provide, e.g. http://aroma-project.org/howtos.
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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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| == Plugins Developers ==
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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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