Question

Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR

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A ▴ 40

@a-14337

Last seen 12 months ago

United Kingdom

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!

isoformswitchanalyzer isoform differential isoform usage • 1.5k views

ADD COMMENT • link written 6.0 years ago by A ▴ 40

score 0 · Answer 1 · 2018-12-06

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k.vitting.seerup ▴ 120

@kvittingseerup-7956

Last seen 15 months ago

European Union

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 COMMENT • link 6.0 years ago k.vitting.seerup ▴ 120

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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 REPLY • link 6.0 years ago A ▴ 40

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