User: rc1253

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rc12530
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Posts by rc1253

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Comment: C: TopTable vs DecideTests: can I just extract DEs with decidetest rowsums !=0?
... Hi Aaron, Thanks again for the detailed response, you're a great help to this bioinformatics newbie! I did indeed run a contrast matrix: contr.matrix <- makeContrasts( tp09 = Infected_09 - Mock_09, tp12 = Infected_12 - Mock_12, tp15 = Infected_15 - Mock_15, tp18 = Infecte ...
written 9 days ago by rc12530
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Comment: C: TopTable vs DecideTests: can I just extract DEs with decidetest rowsums !=0?
... Hi Aaron, Thank you for the response. My design is: z <- two conditions across 16-time points. design <- model.matrix(~0 + z) (basically testing DE at each time point between control and treated conditions) That makes sense about them having a different hypothesis, decidetests is probabl ...
written 10 days ago by rc12530
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TopTable vs DecideTests: can I just extract DEs with decidetest rowsums !=0?
... Hi everyone, I am looking for critique on the methods I've used to find DEGs in my data. I initially used Ebayes with 'BH' FDR adjustment but found this stringency wasn't enough. I switched to trying bonferroni but had issues with my decidetests and toptable results not matching? dt <-decideT ...
limma written 10 days ago by rc12530 • updated 10 days ago by Aaron Lun22k

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