User: fiona.dick91

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fiona.dick9110
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Posts by fiona.dick91

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DRIMSeq continious variable in design matrix - Error during precision estimation
... 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 ...
drimseq dmprecision written 6 weeks ago by fiona.dick9110
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Comment: C: stageR NA in getAdjustedPValues() (method=dtu)
... 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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rnaseqDTU DTU workflow - pots-hoc Filter
... 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 ...
drimseq dtu rnaseqdtu written 9 weeks ago by fiona.dick9110 • updated 9 weeks ago by Michael Love22k
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rnaseqDTU log2fold change DEXSeq
... 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 ...
dexseq salmon drimseq dtu log2fold written 9 weeks ago by fiona.dick9110
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Comment: C: stageR NA in getAdjustedPValues() (method=dtu)
... perfect, I tried it right away and it works. Thanks a lot! ...
written 8 months ago by fiona.dick9110
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Comment: C: stageR NA in getAdjustedPValues() (method=dtu)
... the error message persists, after updating as you recommended.   ...
written 8 months ago by fiona.dick9110
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Comment: C: stageR NA in getAdjustedPValues() (method=dtu)
... 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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Comment: C: stageR NA in getAdjustedPValues() (method=dtu)
... 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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stageR NA in getAdjustedPValues() (method=dtu)
... 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 ...
drimseq dtu salmon rna seq stager written 8 months ago by fiona.dick9110 • updated 8 months ago by Koen Van den Berge170

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