A simple procedure for estimating the false discovery rate.
BACKGROUND
The most used criterion in microarray data analysis is nowadays the false discovery rate (FDR). In the framework of estimating procedures based on the marginal distribution of the P-values without any assumption on gene expression changes, estimators of the FDR are necessarily conservatively biased. Indeed, only an upper bound estimate can be obtained for the key quantity pi0, which is the probability for a gene to be unmodified. In this paper, we propose a novel family of estimators for pi0 that allows the calculation of FDR.


RESULTS
The very simple method for estimating pi0 called LBE (Location Based Estimator) is presented together with results on its variability. Simulation results indicate that the proposed estimator performs well in finite sample and has the best mean square error in most of the cases as compared with the procedures QVALUE, BUM and SPLOSH. The different procedures are then applied to real datasets.


BACKGROUND
The R function LBE is available at http://ifr69.vjf.inserm.fr/lbe


BACKGROUND
broet@vjf.inserm.fr.
INSERM U472, Faculté de Médecine Paris-Sud 16 Avenue Paul Vaillant-Couturier, 94807 Villejuif Cedex, France.
Cyril
C
Dalmasso
Philippe
P
Broët
Thierry
T
Moreau
D000465:Algorithms; D014408:Biomarkers, Tumor / Q000378:metabolism; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D003936:Diagnosis, Computer-Assisted / Q000379:methods; D005189:False Positive Reactions; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007938:Leukemia / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D015233:Models, Statistical; D009363:Neoplasm Proteins / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins