Literature DB >> 17586828

beadarray: R classes and methods for Illumina bead-based data.

Mark J Dunning1, Mike L Smith, Matthew E Ritchie, Simon Tavaré.   

Abstract

UNLABELLED: The R/Bioconductor package beadarray allows raw data from Illumina experiments to be read and stored in convenient R classes. Users are free to choose between various methods of image processing, background correction and normalization in their analysis rather than using the defaults in Illumina's; proprietary software. The package also allows quality assessment to be carried out on the raw data. The data can then be summarized and stored in a format which can be used by other R/Bioconductor packages to perform downstream analyses. Summarized data processed by Illumina's; BeadStudio software can also be read and analysed in the same manner. AVAILABILITY: The beadarray package is available from the Bioconductor web page at www.bioconductor.org. A user's guide and example data sets are provided with the package.

Mesh：

Year:  2007        PMID： 17586828     DOI： 10.1093/bioinformatics/btm311

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  261 in total

1.  T cell and APC dynamics in situ control the outcome of vaccination.

Authors:  Kamal M Khanna; David A Blair; Anthony T Vella; Stephen J McSorley; Sandip K Datta; Leo Lefrançois
Journal:  J Immunol       Date:  2010-06-07       Impact factor: 5.422

Review 2.  Statistical approaches for the analysis of DNA methylation microarray data.

Authors:  Kimberly D Siegmund
Journal:  Hum Genet       Date:  2011-04-26       Impact factor: 4.132

3.  Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage.

Authors:  Lukas Chavez; Justyna Jozefczuk; Christina Grimm; Jörn Dietrich; Bernd Timmermann; Hans Lehrach; Ralf Herwig; James Adjaye
Journal:  Genome Res       Date:  2010-08-27       Impact factor: 9.043

4.  Integration of genetic signature and TNM staging system for predicting the relapse of locally advanced colorectal cancer.

Authors:  Junjie Peng; Zhimin Wang; Wei Chen; Yin Ding; Haifeng Wang; Hongjie Huang; Wei Huang; Sanjun Cai
Journal:  Int J Colorectal Dis       Date:  2010-08-13       Impact factor: 2.571

5.  In vivo cell-autonomous transcriptional abnormalities revealed in mice expressing mutant huntingtin in striatal but not cortical neurons.

Authors:  Elizabeth A Thomas; Giovanni Coppola; Bin Tang; Alexandre Kuhn; SoongHo Kim; Daniel H Geschwind; Timothy B Brown; Ruth Luthi-Carter; Michelle E Ehrlich
Journal:  Hum Mol Genet       Date:  2010-12-20       Impact factor: 6.150

6.  Multi-level mixed effects models for bead arrays.

Authors:  Ryung S Kim; Juan Lin
Journal:  Bioinformatics       Date:  2010-12-17       Impact factor: 6.937

7.  Modification of T cell responses by stem cell mobilization requires direct signaling of the T cell by G-CSF and IL-10.

Authors:  Kelli P A MacDonald; Laetitia Le Texier; Ping Zhang; Helen Morris; Rachel D Kuns; Katie E Lineburg; Lucie Leveque; Alistair L Don; Kate A Markey; Slavica Vuckovic; Frederik O Bagger; Glen M Boyle; Bruce R Blazar; Geoffrey R Hill
Journal:  J Immunol       Date:  2014-02-28       Impact factor: 5.422

8.  MicroRNA expression signatures and their correlation with clinicopathological features in glioblastoma multiforme.

Authors:  Michael Henriksen; Kasper Bendix Johnsen; Pia Olesen; Linda Pilgaard; Meg Duroux
Journal:  Neuromolecular Med       Date:  2014-05-10       Impact factor: 3.843

9.  Impaired toll-like receptor 3-mediated immune responses from macrophages of patients chronically infected with hepatitis C virus.

Authors:  Feng Qian; Christopher R Bolen; Chunxia Jing; Xiaomei Wang; Wei Zheng; Hongyu Zhao; Erol Fikrig; R Douglas Bruce; Steven H Kleinstein; Ruth R Montgomery
Journal:  Clin Vaccine Immunol       Date:  2012-12-05

10.  Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis.

Authors:  Kristina Becanovic; Mahmoud A Pouladi; Raymond S Lim; Alexandre Kuhn; Paul Pavlidis; Ruth Luthi-Carter; Michael R Hayden; Blair R Leavitt
Journal:  Hum Mol Genet       Date:  2010-01-20       Impact factor: 6.150
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