Question: Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
1
gravatar for A
6 months ago by
A40
A40 wrote:

Hi all, 

 

Quick question, I was wondering if it possible to use directly, the output of a DEXSeq analysis and pass it in to analysis for isoformswitchanalyzeR? I have looked but cant find any information on this....

 

If so, which step can it be picked up from in the vignette?

 

Many thanks!

ADD COMMENTlink modified 6 months ago by k.vitting.seerup90 • written 6 months ago by A40
Answer: Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
0
gravatar for k.vitting.seerup
6 months ago by
European Union
k.vitting.seerup90 wrote:

Nope. But what you can do is use IsoformSwitchAnalyzeR to run DEXSeq - acutally DEXSeq is the default statistical engine (via the isoformSwitchTestDEXSeq() function) so you can just start from the top of the vignette.

Please note that if you have >2 conditions IsoformSwitchAnalyzeR will do all pariwise comparisons (as opposed to DEXSeq which performing a single ANOVA-style test). 

Let me know if you have more questions :-)

Cheers

Kristoffer

ADD COMMENTlink modified 6 months ago • written 6 months ago by k.vitting.seerup90

Thank you so much for the quick response! I guess one quick follow up question... As im not too familiar with the command line alignment tools, can a feature counts output (counts over exons) be passed to IsoformSwitchAnalyzeR. Would that suffice as a counts table?

 

Thanks again!

ADD REPLYlink written 6 months ago by A40

Unfortunatly not - you need transcript expression. That can be done with the tools discussed in the vignette here.

ADD REPLYlink written 6 months ago by k.vitting.seerup90

Thank you!!

ADD REPLYlink written 6 months ago by A40
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