Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

CBS >> CBS Bioinformatics Tools >> Jetset

jetset logo



Jetset: selecting an optimal microarray probe set to represent a gene
Qiyuan Li, Nicolai J. Birkbak, Balazs Gyorffy, Zoltan Szallasi, and Aron C. Eklund
BMC Bioinformatics 2011, 12:474

Summary: On Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets which may deliver inconsistent or even contradictory measurements. Therefore, obtaining an unambiguous expression estimate of a pre-specified gene can be nontrivial. We developed scoring methods to assess each probe set for specificity, coverage, and degradation resistance. We used these scores to select the optimal probe set for each gene, and thus create a simple one-to-one mapping between gene and probe set.

Release information

The jetset algorithm utilizes two sources of external data:
  • mRNA sequences from RefSeq
  • RefSeq-to-gene mappings from the R/Bioconductor package org.Hs.eg.db.

Data source version
Version Release RefSeq org.Hs.eg.db Notes
0.99.0 04 August, 2010 21 March, 2010 2.4.1
0.99.1 22 August, 2011 17 August, 2011 2.5.0 Buggy version
0.99.2 25 August, 2011 17 August, 2011 2.5.0 Bug fix, improved implementation, different CSV format
0.99.3 28 November, 2011 24 November, 2011 2.6.4
1.0.0 2 May, 2012 29 April, 2012 2.7.1
1.2.0 5 October, 2012 2 October, 2012 2.8.0
1.4.0 24 April, 2013 22 April, 2013 2.9.0
1.6.0 25 November, 2013 21 November, 2013 2.10.1
2.14.0 18 April, 2014 17 April, 2014 2.14.0 Version numbers are now synchronized with org.Hs.eg.db
3.0.0 10 November, 2014 6 November, 2014 3.0.0

Easy installation of the R package

If you are using a recent version of R (>= 3.1.1), the easiest way to install the package is directly from the URL:

Windows:

install.packages('http://www.cbs.dtu.dk/biotools/jetset/current/jetset_3.0.0.zip', repos = NULL)

Everyone else:

install.packages('http://www.cbs.dtu.dk/biotools/jetset/current/jetset_3.0.0.tar.gz', repos = NULL, type = 'source')

Download the R package

If the easy installation doesn't apply to you, you can download the latest package from below, and then install it manually:

Source (unix) jetset_3.0.0.tar.gz
Windows jetset_3.0.0.zip

Data in CSV format

Current versions can be downloaded from the following table. The data in the CSV files and the data in the R package are essentially identical. The CSV files are intended for people who don't use R.

Platform Probe set score file
HG-U95Av2 jetset.scores.hgu95av2_3.0.0.csv.zip
HG-U133A jetset.scores.hgu133a_3.0.0.csv.zip
HG-U133 Plus 2.0 jetset.scores.hgu133plus2_3.0.0.csv.zip
U133 X3P jetset.scores.u133x3p_3.0.0.csv.zip

Previous versions can be downloaded here.
Users of these files may be interested in a brief explanation of the data format.

Related works



CORRESPONDENCE

      

This file was last modified Monday 10th 2014f November 2014 13:54:54 GMT