DRIMSeq with technical replicates
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@poecilepal-22574
Last seen 3.1 years ago
Russia

Good afternoon,

I use DRIMSeq-workflow from this page http://bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html#statistical-analysis-of-differential-transcript-usage to explore differential transcript usage. Could you please point me out, where and how should I collapse technical replicates in DRIMSeq? For example, for DEG search in DESeq2 I use collapseReplicates function before running DESeq.

Best regards, Poecile palustris
DRIMSeq R DTU technical replicates deseq2 • 1.4k views
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Cross-posted: https://www.biostars.org/p/450220/

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Hello Kevin,

Yes, thanks, I have duplicated this post on another forum just in case.

Best regards, Poecile palustris

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Oh, I read about disadvantages of cross-hosting, I apologize for my ignorance. It seems that post https://www.biostars.org/p/450220/ has already been deleted.

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Kevin Blighe ★ 4.0k
@kevin
Last seen 6 weeks ago
Republic of Ireland

It seems that the DRIMSeq authors have not yet checked - you may consider contacting them. Also, you could still use the DESeq2 functionality here and then export the 'collapsed' counts (via counts(dds, normalised = FALSE)) for use with DRIMSeq. You could also apply your own function manually for collapsing your replicates.

Kevin
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Thank you very much for your response! I used DESeq2 functionality: firstlycollapseReplicates function from DESeq2, then divided each value by the number of replicates.

Best regards, Poecile palustris

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