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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.
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Data source version |
| Version |
Release |
RefSeq |
org.Hs.eg.db |
Notes |
| 0.99.0 |
04 August, 2010 |
21 March, 2010 |
2.4.1 |
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| 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 |
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| 1.0.0 |
2 May, 2012 |
29 April, 2012 |
2.7.1 |
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| 1.2.0 |
5 October, 2012 |
2 October, 2012 |
2.8.0 |
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| 1.4.0 |
24 April, 2013 |
22 April, 2013 |
2.9.0 |
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| 1.6.0 |
25 November, 2013 |
21 November, 2013 |
2.10.1 |
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| 2.14.0 |
18 April, 2014 |
17 April, 2014 |
2.14.0 |
Version numbers are now synchronized with org.Hs.eg.db |
The R package
We hope to distribute the jetset R package through Bioconductor. Until this is arranged, the package can be downloaded here:
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.
Related works
CORRESPONDENCE
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