User: gosia.nowicka

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Posts by gosia.nowicka

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Answer: A: DEXSeq and DRIMSeq on paired samples?
... In DRIMSeq, based on the design matrix, you would set the full model as design_full <- model.matrix(~ cond + pair, data = samples(d)) and use it in dmPrecision() and dmFit(). In dmTest(), you can specify which coefficient you would like to test with coef = "condpre" or coef = "condpost", depen ...
written 24 days ago by gosia.nowicka30
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Comment: C: stageR NA in getAdjustedPValues() (method=dtu)
... Hello Fiona, I am very sorry for my late reply. You have mentioned that the design matrix from DRIMSeq output is different than what you feed in. Would you like that I have a look on that? If yes, would share with me the d object after running the analysis? You could send it to gosia.nowicka@uzh.ch ...
written 11 weeks ago by gosia.nowicka30
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Answer: A: Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
... Dear Kristoffer,  I am glad you find DRIMSeq useful.  I have been working on implementing the isoform-level analysis which are based on the beta-binomial distribution.  Additionally, there will be a full regression framework available for gene-level and feature-level analysis allowing for modelin ...
written 20 months ago by gosia.nowicka30

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