## User: fiona.dick91

fiona.dick9110
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#### Posts by fiona.dick91

<prev • 9 results • page 1 of 1 • next >
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... Hi, I tried to use DRIMSeq to test for DTU given a design matrix that looks like this: (this is just an example, I have (49 samples) [1] "DESIGN: Formula:" ~condition + cov1 + cov2 [1] "Design matrix:" (Intercept) condition cov1 cov2 1 1 86 6.4 0 ...
written 6 weeks ago by fiona.dick9110
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... Hi! sorry for the late answer I totally forgot about this thread. It was my own mistake because I called the design matrix of the reduced model...So all is good. Thanks for the help ...
written 6 weeks ago by fiona.dick9110
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... Hi, I have been following the DTU workflow which is linked to the package rnaseqDTU and the paper: "Swimming downstream: statistical analysis of differential transcript usage following Salmon" https://f1000research.com/articles/7-952/v3 It is mentioned that, in favor of controlling the FDR of DR ...
written 9 weeks ago by fiona.dick9110 • updated 9 weeks ago by Michael Love22k
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... I have a general quesiton concerning the described workflow of "rnaseqDTU" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178912.3/pdf/f1000research-7-17982.pdf I have followed the workflow to test for DTU on count data generated by salmon. Just as described in the workflow, I have imported them wi ...
written 9 weeks ago by fiona.dick9110
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... perfect, I tried it right away and it works. Thanks a lot! ...
written 8 months ago by fiona.dick9110
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... the error message persists, after updating as you recommended.   ...
written 8 months ago by fiona.dick9110
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... I sent you the result object from the DRIMSeq analysis. the data for stageR would then be: pScreen <- res$res$adj_pvalue pConfirmation <- res$txp$adj_pvalue tx2gene <- res\$res[,c("feature_id","gene_id")]   ...
written 8 months ago by fiona.dick9110
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... thanks for the quick reply. I will update the package and try with the new version. How could I share a subset of my data to make as much sense as possible? would you like to have the imported and scaled abundances of a subset of transcripts and a subset of samples? ...
written 8 months ago by fiona.dick9110
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... Hello, Im working with DRIMSeq and stageR to analyse DTU from RNASeq transcript counts estimated by salmon. I have been following DRIMSeq and stagR's vignette. Importing my reads with tximport, using scaledTPM as scaling method. Filtering transcripts according to recommendations and calculating pr ...
written 8 months ago by fiona.dick9110 • updated 8 months ago by Koen Van den Berge170

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