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Question: Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
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gravatar for A
11 days ago by
A10
A10 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 11 days ago by k.vitting.seerup30 • written 11 days ago by A10
0
gravatar for k.vitting.seerup
11 days ago by
European Union
k.vitting.seerup30 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 11 days ago • written 11 days ago by k.vitting.seerup30

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 11 days ago by A10

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

ADD REPLYlink written 11 days ago by k.vitting.seerup30

Thank you!!

ADD REPLYlink written 10 days ago by A10
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