User: fiona.dick91

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fiona.dick9110
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Posts by fiona.dick91

<prev • 16 results • page 1 of 2 • next >
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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 13 days 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 15 days 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 15 days 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 21 days 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 28 days 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 7 weeks 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 7 weeks ago by fiona.dick9110 • updated 7 weeks ago by Michael Love23k
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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 3 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 3 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 4 months ago by fiona.dick9110 • updated 4 months ago by Michael Love23k

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