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Old 09-15-2014, 01:02 PM   #1
wacguy
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Location: NC

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Default edgeR contrast

I've noticed that:

lrt <- glmLRT(fit, contrast=c(-1,1,0))

vs

lrt <- glmLRT(fit, contrast=c(1,-1,0))
gives you different set of genes. How do I decide about the order (1, -1 or -1, 1); I just want to extract the DEGs between 2 conditions.

Thanks a lot, Guy
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Old 09-22-2014, 07:02 PM   #2
Gordon Smyth
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No it doesn't.

Using 1,-1 instead of -1,1 gives exactly the same genes just with logFC of opposite sign.
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Old 09-22-2014, 07:24 PM   #3
wacguy
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Thank you Gordon, I finally figured it out too.


Guy
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