User: fiona.dick91

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fiona.dick9110
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Posts by fiona.dick91

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Comment: C: DEXSeq dispersion outlier
... yes, I did try. I also changed the volcano plot to use the condition coefficient as l2fc instead of the result of DEXSeq::estimeExonFoldChange. There still remain some outliers but its not the same transcripts. Here you can find both volcano plots. The one resulting from analysis with and one withou ...
written 9 weeks ago by fiona.dick9110
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Comment: C: DEXSeq dispersion outlier
... thanks again for your detailed answer. - the counts from `DEXSeq::featureCounts` are the raw ones and not the fitted ones, right? - Sorry for asking again, I dont understand your point with the covariates. We neither see sth when looking at the fitted nor the raw counts, right? And even if the ...
written 9 weeks ago by fiona.dick9110
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Comment: C: DEXSeq dispersion outlier
... Hi, thanks for replying. - I have attached the plot you have described for the six outliers that i have reported above (in the .rds file): https://drive.google.com/file/d/1VKSjamZMHjLYWsYL6YH3t_zrABNRSaQ-/view?usp=sharing ( counts from `DEXSeq::featureCounts`, added pseudocount and the took the lo ...
written 9 weeks ago by fiona.dick9110
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DEXSeq dispersion outlier
... Hi, I have been using DEXSeq with transcript counts from salmon (as suggested in e.g. : https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0862-3 ) to investigate DTU between conditions case vs control. I followed a workflow described in: https://f1000research.com/articles/7-952/v ...
dexseq pvalue dispersion written 10 weeks ago by fiona.dick9110
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Comment: C: rnaseqDTU DTU workflow - pots-hoc Filter
... Thanks for the answer and sorry for late answer. Is it ok to perform post-hoc filter on lfc transcripts *after* testing and reporting the unchanged pvalue? Is it ok to use `DEXSeq::estimateExonFoldChange` and `DRIMSeq::coefficients` for this purpose if Id want to do the same post hoc filtering on b ...
written 11 weeks ago by fiona.dick9110
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Comment: C: dtuScaledTPM vs lengthScaledTPM in DTU analysis
... thanks for taking the time to answer. so the main difference to `lengthScaledTPM` is, that you take the average overall samples: > "Since all TPMs for all samples within a gene are scaled by the same value" and so you do not unpuprosley set down the whole gene expression, in one sample (groupA) ...
written 3 months ago by fiona.dick9110
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dtuScaledTPM vs lengthScaledTPM in DTU analysis
... Hi, I have a question concerning the "new" scaling method offered by `tximport` called `dtuScaledTPM` and how it affects DTU analysis. So far I have used `scaledTPM` which as I understand (correct me if Im wrong) scales the TPM values to library size by multiplying the TPM of a transcript of a samp ...
salmon tpm tximport dtu rnaseqdtu written 3 months ago by fiona.dick9110 • updated 3 months ago by Michael Love24k
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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 5 months 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 5 months 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 6 months ago by fiona.dick9110 • updated 6 months ago by Michael Love24k

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