User: rbenel

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rbenel0
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Posts by rbenel

<prev • 51 results • page 1 of 6 • next >
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Comment: C: stageR following DEXSeq two-stage analysis
... OK. Thank you for the detailed answer. ...
written 4 months ago by rbenel0
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Comment: C: stageR following DEXSeq two-stage analysis
... Yes, my question was how there can be evidence for a single transcript when in order for DTU to occur by definition there needs to be another transcript involved. I understand that there is a distinction between the underlying proportions v. statistical testing. So, what would you suggest one do w ...
written 4 months ago by rbenel0
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Comment: C: stageR following DEXSeq two-stage analysis
... Also, as a side note, what would be considered the minimum read depth for DTU detection? ...
written 4 months ago by rbenel0
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Comment: C: stageR following DEXSeq two-stage analysis
... I can look for a clearer case, but if the expression looks roughly similar, than I should not have gotten even a single significant transcript..? The error bars are SD. I "filtered" just to make my own script clear, but from the workflow, "The final table with adjusted p-values summarizes the inf ...
written 4 months ago by rbenel0
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stageR following DEXSeq two-stage analysis
... After running the `dex.padj <- getAdjustedPValues(stageRObj, order=FALSE, onlySignificantGenes=TRUE)`, and filtering for only the transcripts in the final table that are less than 0.05 I received a list of genes with only 1 transcript that was significant. I was curious to see what the expressi ...
rnaseqdtu written 4 months ago by rbenel0
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Comment: C: Differential transcript expression (DTE) analysis
... Yes, a total switch would be the most biologically interesting in this case... If something comes of the analysis I can post the code here in case it interests anyone else. Thanks Michael for all of the help :) ...
written 4 months ago by rbenel0
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Comment: C: Differential transcript expression (DTE) analysis
... You are reading it correctly, and yes there is a change in the proportion, but the global picture suggests that the major isoform is decreasing with time (regardless of its relationship to the minor isoform). Therefore, I am not sure that the increase in the minor isoform between day 0 and day 1 is ...
written 4 months ago by rbenel0
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Comment: C: Differential transcript expression (DTE) analysis
... OK. I understand that the middle area can be both DGE and DTU. In the specific example, I was concerned about the evidence for DTU, it doesn't seem to me that there is a large change in isoform proportions, that's all. ...
written 4 months ago by rbenel0
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Comment: C: Differential transcript expression (DTE) analysis
... Just to clarify, "For the DTE analysis you are getting a p-value for DE of each transcript" means if you use a DGE method on transcript level data, you should be getting a p-value for every transcript that is DE? In addition, I have a question regarding the link I posted with an example, it seems ...
written 4 months ago by rbenel0
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Comment: C: Differential transcript expression (DTE) analysis
... As a follow up, here is an example of a gene that is DGE following DESeq2, and also has two transcripts that are DTU following DEXseq and stageR analysis with a significant adjusted p-value at the level of the gene and transcript. bargraph: https://www.dropbox.com/s/z95ri9keyt48bcw/example_biocondu ...
written 5 months ago by rbenel0

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