User: rc1253

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rc12530
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Posts by rc1253

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Plotting consensus eigengene networks for specific interesting modules?
... I have followed to typical WGCNA workflow and produced an eigengene network for the consensus modules. However, after TopGO analysis I have identified some interesting modules. Instead of producing a noisy plot with all my modules - is there a way to only plot modules for my selected ones? Here's ...
wgcna written 10 weeks ago by rc12530
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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 5 months 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 5 months 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 5 months ago by rc12530 • updated 5 months ago by Aaron Lun24k

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