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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? ====
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| Better not.
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| ==== Can I install multiple versions of R? ====
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| Yes.
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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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| == 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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| === Check BRB-ArrayTools message board [http://linus.nci.nih.gov/cgi-bin/brb/board1.cgi] ===
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