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
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.
The jetset algorithm utilizes two sources of external data:
- mRNA sequences from
- RefSeq-to-gene mappings from the R/Bioconductor package
||Data source version
||04 August, 2010
||21 March, 2010
||22 August, 2011
||17 August, 2011
||25 August, 2011
||17 August, 2011
||Bug fix, improved implementation, different CSV format
||28 November, 2011
||24 November, 2011
||2 May, 2012
||29 April, 2012
||5 October, 2012
||2 October, 2012
||24 April, 2013
||22 April, 2013
||25 November, 2013
||21 November, 2013
||18 April, 2014
||17 April, 2014
||Version numbers are now synchronized with org.Hs.eg.db
||10 November, 2014
||6 November, 2014
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:
install.packages('http://www.cbs.dtu.dk/biotools/jetset/current/jetset_3.0.0.zip', repos = NULL)
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:
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.
Previous versions can be downloaded here.
Users of these files may be interested in a brief explanation of the data format.