oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language

被引：83

作者：

Sanges, Remo

Cordero, Francesca

Calogero, Raffaele A.

机构：

[1] CBM Cluster Biomed ScrI, I-34012 Trieste, Italy

[2] Univ Turin, Dept Informat, I-10149 Turin, Italy

[3] Univ Turin, Dept Clin & Biol Sci, I-10043 Turin, Italy

来源：

BIOINFORMATICS | 2007年 / 23卷 / 24期

关键词：

D O I：

10.1093/bioinformatics/btm469

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

OneChannelGUI is an add-on Bioconductor package providing a new set of functions extending the capability of the affylmGUI package. This library provides a graphical interface (GUI) for Bioconductor libraries to be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays. Affymetrix 3 expression (IVT) arrays as well as the new whole transcript expression arrays, i.e. gene/exon 1.0 ST, are actually implemented. oneChannelGUI is available for most platforms on which R runs, i.e. Windows and Unix-like machines.

引用

收藏

页码：3406 / 3408

页数：3

相关论文

共 13 条

[1] Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments [J].

Breitling, R ;

Armengaud, P ;

Amtmann, A ;

Herzyk, P .

FEBS LETTERS, 2004, 573 (1-3) :83-92

[2] maSigPro:: a method to identify significantly differential expression profiles in time-course microarray experiments [J].

Conesa, A ;

Nueda, MJ ;

Ferrer, A ;

Talón, M .

BIOINFORMATICS, 2006, 22 (09) :1096-1102

[3] Using GOstats to test gene lists for GO term association [J].

Falcon, S. ;

Gentleman, R. .

BIOINFORMATICS, 2007, 23 (02) :257-258

[4]

GENTLEMAN R, 2004, COMPSTAT 2004 P COMP

[5] Bioconductor: open software development for computational biology and bioinformatics [J].

Gentleman, RC ;

Carey, VJ ;

Bates, DM ;

Bolstad, B ;

Dettling, M ;

Dudoit, S ;

Ellis, B ;

Gautier, L ;

Ge, YC ;

Gentry, J ;

Hornik, K ;

Hothorn, T ;

Huber, W ;

Iacus, S ;

Irizarry, R ;

Leisch, F ;

Li, C ;

Maechler, M ;

Rossini, AJ ;

Sawitzki, G ;

Smith, C ;

Smyth, G ;

Tierney, L ;

Yang, JYH ;

Zhang, JH .

GENOME BIOLOGY, 2004, 5 (10)

[6] FLEXIBLE DISCRIMINANT-ANALYSIS BY OPTIMAL SCORING [J].

HASTIE, T ;

TIBSHIRANI, R ;

BUJA, A .

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 1994, 89 (428) :1255-1270

[7] Exploration, normalization, and summaries of high density oligonucleotide array probe level data [J].

Irizarry, RA ;

Hobbs, B ;

Collin, F ;

Beazer-Barclay, YD ;

Antonellis, KJ ;

Scherf, U ;

Speed, TP .

BIOSTATISTICS, 2003, 4 (02) :249-264

[8]

Smyth G. K., 2004, Stat. Appl. Genet. Mol. Biol., DOI 10.2202/1544-6115.1027

[9] Diagnosis of multiple cancer types by shrunken centroids of gene expression [J].

Tibshirani, R ;

Hastie, T ;

Narasimhan, B ;

Chu, G .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (10) :6567-6572

[10] Significance analysis of microarrays applied to the ionizing radiation response [J].

Tusher, VG ;

Tibshirani, R ;

Chu, G .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (09) :5116-5121