To the attention of Bioconductor Help System,

I have a question about the application of FDR cut-off values to gene expression data. When you are looking at different sets of data, can you apply different FDR cut-off values? Sometimes in one experiment you may find that applying an FDR<0.05 yields a very small number of significant changes but if you accept an FDR slighlty higher (<0.075) then you may get a few hundred significant changes. What is the ideal FDR cut-off value? Can you use different FDR cut-off values for different experimental data? For example, if you have two sets of experimentla data:

Experiment 1: 30 Differentially Expressed (DE) genes for an FDR<0.05 or 456 DE genes for an FDR<0.1
Experiment 2: 678 DE genes for an FDR<0.05 or 2398 DE genes for and FDR<0.1

If you want to compare results from the two experiments, is it correct to compare the results with FDR<0.1 from experiment 1 against the results with an FDR<0.05 from experiment 2?

Many thanks for your help

Mayte


Dr. María Teresa García Conesa
Científico Titular
Consejo Superior de Investigaciones Científicas (CSIC)
Centro de Edafología y Biología Aplicada del Segura (CEBAS)
Calidad, Seguridad y Bioactividad de Alimentos Vegetales
Apartado de Correos 164, 30100 Campus de Espinardo
Murcia
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