FIRMA: a method for detection of alternative splicing from exon array data.
BACKGROUND
Analyses of EST data show that alternative splicing is much more widespread than once thought. The advent of exon and tiling microarrays means that researchers now have the capacity to experimentally measure alternative splicing on a genome wide level. New methods are needed to analyze the data from these arrays.


RESULTS
We present a method, finding isoforms using robust multichip analysis (FIRMA), for detecting differential alternative splicing in exon array data. FIRMA has been developed for Affymetrix exon arrays, but could in principle be extended to other exon arrays, tiling arrays or splice junction arrays. We have evaluated the method using simulated data, and have also applied it to two datasets: a panel of 11 human tissues and a set of 10 pairs of matched normal and tumor colon tissue. FIRMA is able to detect exons in several genes confirmed by reverse transcriptase PCR.


BACKGROUND
R code implementing our methods is contributed to the package aroma.affymetrix.
Purdom
E
E
Department of Statistics, University of California at Berkeley, 367 Evans Hall #3860, Berkeley, CA 94720-3860, USA. epurdom@stat.berkeley.edu
Simpson
K M
KM
Robinson
M D
MD
Conboy
J G
JG
Lapuk
A V
AV
Speed
T P
TP
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D022821:RNA Splice Sites / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D022821:RNA Splice Sites