limmaGUI - venn-diagram & top-table anomaly?
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@dlevinwarwickacuk-3666
Last seen 7.2 years ago
Hello, In limmaGUI, after running a linear model for a single gene & time point (mutant vs control), the venn-diagram for differentially expressed genes with a 0.001 p-value cut-off gives a different number than the top- table with the same cut-off (2600 vs. 791). I have seen the same thing happen before for multiple time points (when the venn-diagram is more relevant) Any ideas what is going on? Thanks Danny
limmaGUI limmaGUI • 623 views
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@keith-satterley-1452
Last seen 7.0 years ago
Australia
Hi Danny, I've looked into how these functions were coded. They use different functions to categorize genes, hence the different numbers. The next version of limmaGUI released with R2.10 in October will use similar functions. I will email when the developer version is available that produces matching results for Venn diagrams and toptables. Thanks for pointing this out, cheers, Keith ======================== Keith Satterley limmaGUI maintainer ======================= D.Levin at warwick.ac.uk wrote: > Hello, > > In limmaGUI, after running a linear model for a single gene & time point > (mutant vs control), the venn-diagram for differentially expressed genes > with a 0.001 p-value cut-off gives a different number than the top- table with > the same cut-off (2600 vs. 791). > > I have seen the same thing happen before for multiple time points (when > the venn-diagram is more relevant) > > Any ideas what is going on? > > Thanks > > Danny > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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