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Question: statistics for differential expression: adjusted p-values<0.05 BUT negative B-odds?
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10.0 years ago by
Christine Voellenkle90 wrote:
modified 10.0 years ago by Paolo Innocenti320 • written 10.0 years ago by Christine Voellenkle90
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10.0 years ago by
Paolo Innocenti320 wrote:
> What makes me worry is that in my statistics I have low adj.p-value 0.03 > together with negative B-values. > How do I have to handle this discrepance? Is this a hint that something is > wrong with my normalization? In the limma userguide they also say: "The B-statistic is automatically adjusted for multiple testing by assuming that 1% of the genes, or some other percentage specified by the user in the call to eBayes(), are expected to be differentially expressed." and "The B-statistic probabilities depend on the same assumptions but require in addition a prior guess for the proportion of differentially expressed genes." So I think your problem is that the number of differentially expressed genes in your experiment is higher that the proportion eBayes assumes (proportion=0.01) Try to specify it in eBayes like this: fit <- eBayes(fit, proportion= <proportion of="" d.e.="" genes="">) and see if you get an improvement, and look at ?eBayes for more information. I never used limmaGUI though, so I don't know how to do it with this interface. I hope this helps. Best, paolo -- Paolo Innocenti Department of Animal Ecology, EBC Uppsala University Norbyv?gen 18D 75236 Uppsala, Sweden