Question: How to obtain up/down regulation column for DEG edgeR results
0
gravatar for cadeans
2.7 years ago by
cadeans0
cadeans0 wrote:

Hi All,

I've gone through and done all my contrasts for a rather large DE experiment using edgeR. I have logFC, logCPM, LR, PValue, and FDR for each of these contrasts but I can't figure out how to add a column that shows up/down regulation for each of my DEGs. I've tried extracting this information using 

> updown.12Cvs24C<-decideTestsDGE(lrt.12Cvs24C, p.value=0.05)

and then adding this column to the results tables using cbind, but I don't think the up/down values are correctly corresponding to the right genes because I have a list of the DEGs (filtered for an FDR < 0.05) that show SAME (0) up/down regulation. If the FDR of these genes is < 0.05 (like the 6 genes shown below), it means that there expression was either significantly higher or lower in one group vs the other, yet the UpDown column doesn't reflect this.

  geneID    logFC      logCPM       LR       PValue         FDR            UpDown
237542  -5.901809 2.871127 41.81711 1.002224e-10 5.653145e-07      0
1879515 -6.603091 5.203004 41.70325 1.062322e-10 5.653145e-07      0
1207284 -6.666918 4.879160 40.38631 2.083963e-10 7.393207e-07      0
131752  -5.096021 7.731907 37.80230 7.828952e-10 2.049564e-06     -1
29878   -6.932289 6.619459 37.25548 1.036232e-09 2.049564e-06      0
483711  -8.104056 7.199398 37.02868 1.164046e-09 2.049564e-06      0

Is there an easy way to extract this information and add it to the results table or do most people just infer it from the logFC values that are already present in the results table? FYI- not an R wiz so be gentle.

Bonus question (while i have your attention): Is there an easy way to isolate the DEGs that are similar between two groups (different contrasts). I know this can be done easily in Galaxy but I'd like to learn it in R. So far can't find a lot about this kind of action.

thanks,

carrie

deg edger • 1.2k views
ADD COMMENTlink written 2.7 years ago by cadeans0
2
gravatar for fubar
2.7 years ago by
fubar1.1k
Australia
fubar1.1k wrote:

edgeR is a Bioconductor package so the Bioconductor package support site https://support.bioconductor.org/ is a better place to search for an answer and if necessary, post your question, than here on a Galaxy forum. The edgeR package maintainers hang around there and answer (good) questions readily - eg see https://support.bioconductor.org/p/47439/

That said, up vs down is trivially determined by the sign of log fold change ignoring "statistical significance" of the change. Direction depends on which group was the reference of course.

In your example all those contigs are *down regulated* since they all have -ve log fold changes but you've tested for "significant" changes which is a completely different ball of wax.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by fubar1.1k

Thanks for the suggestion. I will definitely do that.

 

carrie

ADD REPLYlink written 2.7 years ago by cadeans0
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