Choosing results from LIMMA analysis
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
Dear Sharon, You are asking to be told that one method is always best, but if there was such a method then the alternatives wouldn't be provided in the software. Different methods provide better power against different types of alternatives. You might start by searching the mailing list archives for comments on the different methods. Best wishes Gordon Original message: [BioC] Choosing results from LIMMA analysis Sharon sharonanandhi at gmail.com Wed Aug 2 14:32:08 CEST 2006 Hi All, I have used limma to analyze the time course microarray data (ctrl, 3Hr, 12Hr and 24Hr; each having 3 arrays). Using eBayes(), I have calculated F.p.value and it's corresponding FDR using p.adjust. I also used 'decideTests(fit1, method="nestedF", adjust.method="BH")'. Now I can choose probesets based on FDR calculated by p.adjust or by using results given by 'nestedF'. I can clearly see that the number of significant probesets given by 'nestedF' is larger than by 'FDR calculated by p.adjust' at the same cutoff value 0.05. Which one is the preferred method for choosing significant probesets? Your suggestions are greatly appreciated. Thanks, Sharon
Microarray limma Microarray limma • 575 views
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