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6 weeks ago by
dennism92510 wrote:

Hey, I was wondering where I could find more information on the resultsNames(). I've read the function's respective manual (i.e ?results) and "Differential expression, manipulation, and visualization of RNA-seq reads" (link) but I still feel a bit lost. I definitely could have missed vital information, so if there isn't any additional, available information, directing me towards crucial sections of the manual would really helpful. For clarification these are my variables...

design = ~Condition + Condition:Treatment

> resultsNames(dds)
[1] "Intercept"                "Condition_res_vs_sen"
[3] "Conditionsen.TreatmentCB" "Conditionres.TreatmentCB"

> levels(dds$Treatment) [1] "DMSO" "CB" > levels(dds$Condition)
[1] "sen" "res"


res = resistant sen = sensitive DMSO and CB are a drug treatments DMSO and sen are the refs

To really specify my confusion it is mainly the results names [3] and [4], but it would be nice to know information and methods behind names

deseq2 • 109 views
modified 6 weeks ago • written 6 weeks ago by dennism92510
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This might be a good read

Yes, that is useful, I highly recommend at least using the bit of code to make a fake data set to try everything on. Note that changing the design can radically change what the resultsNames entries will return, so it's good to make a test, to make sure to confirm in Excel that you are getting the log fold changes that you expect. Personally I prefer to use the contrast arguments instead of name whenever possible, because they work as expected even if you forgot to change the reference levels, and it's just easier down the road to figure out what's you compared to what.

Note that some of the comparisons, like comparing WT condition1 to WT condition 2, are much simpler to accomplish using the method here: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions

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6 weeks ago by
Kevin Blighe160
Kevin Blighe160 wrote:

Type ?results and read through the manual entry that appears. Then, you will understand better the output of the resultsNames command.