SScore: an R package for detecting differential gene expression without gene expression summaries.
CONCLUSIONS
SScore is an R package that facilitates the comparison of gene expression between Affymetrix GeneChips using the S-score algorithm. The S-score algorithm uses probe level data directly to assess differences in gene expression, without requiring a preliminary separate step of probe set expression summary estimation. Therefore, the algorithm avoids introduction of error associated with the expression summary estimation process and has been demonstrated to improve the accuracy of identifying differentially expressed genes. The S-score produces accurate results even when few or no replicates are available.


BACKGROUND
The R package SScore is available from Bioconductor at http://www.bioconductor.org
Kennedy
Richard E
RE
Department of Biostatistics, Virginia Commonwealth University Box 980032, Richmond, VA 23298-0032, USA. rkennedy@vcu.edu
Kerns
Robnet T
RT
Kong
Xiangrong
X
Archer
Kellie J
KJ
Miles
Michael F
MF
D000465:Algorithms; D001185:Artificial Intelligence; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface