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User: Koen Van den Berge

Reputation:
170
Status:
Trusted
Location:
Ghent University, Belgium
Last seen:
3 weeks, 2 days ago
Joined:
5 years ago
Email:
k***********@gmail.com

Posts by Koen Van den Berge

<prev • 33 results • page 1 of 4 • next >
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Comment: C: stageR: Error in stageWiseAdjustment
... Yes, the different annotations have been a problem for `stageR`, and I apologize for this inconvenience. This should be fixed in the following major upgrade of the package. Let us know, on the BioC support site, if you have any additional questions. ...
written 23 days ago by Koen Van den Berge170
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Comment: C: stageR: Error in stageWiseAdjustment
... Yes, the different annotations have been a problem for `stageR`, and I apologize for this inconvenience. This should be fixed in the following major upgrade of the package. Let us know, on the BioC support site, if you have any additional questions. ...
written 23 days ago by Koen Van den Berge170
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Comment: C: Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
... Yes, two stageR analyses would be appropriate in that case, and you are correct that according to Shaffer's procedure, you are allowed to not adopt a FWER correction in the confirmation stage, so indeed `method="none"` will be valid here. ...
written 4 weeks ago by Koen Van den Berge170
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Answer: A: Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
... If you would want to analyze both timepoints and all treatments in a single stage-wise analysis, you would have two options: - A three-stage analysis: (i) Global screening test to assess differences between any of the treatments in any of the timepoints. (ii) Conditional on rejecting (i) you may p ...
written 5 weeks ago by Koen Van den Berge170
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Comment: C: ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like t
... Thank you for checking this. In the zinbFit function, could you specify your treatment design as well? This will allow the zero excess probability to systematically vary with the treatment. Also, we recommend setting commondispersion=TRUE. In the meanwhile, I would be happy to take a look at the da ...
written 6 months ago by Koen Van den Berge170
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Comment: C: ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like t
... I agree with Mike's suggestions, and would check those first. In addition, could you also let us know how the weights look like for the zeros of those specific genes? Can you share some of your code, e.g. did you include the treatment effect in the ZINB-WaVE model? Note that in our simulations, we ...
written 6 months ago by Koen Van den Berge170
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Answer: A: stageR NA in getAdjustedPValues() (method=dtu)
... Hi Fiona, I found out that the error stems back from the gene-level p-values that do not carry the names of the genes that they are representing. In your case, the error can be solved by setting names(pScreen)=res[[2]]$gene_id before inputting pScreen in stageR. I will now make sure to give a c ...
written 7 months ago by Koen Van den Berge170
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Comment: C: stageR NA in getAdjustedPValues() (method=dtu)
... I am not yet very familiar with DRIMSeq, but it would be great if you could share your `d` object after running DRIMSeq. From browsing through your code it seems like that should contain most of what I need to run stageR and check where things went wrong. You could for example send it to koen.vanden ...
written 7 months ago by Koen Van den Berge170
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Comment: C: stageR NA in getAdjustedPValues() (method=dtu)
... Thank you for reporting this. There used to be a problem with getAdjustedPValues in the older versions of stageR. It would be great if you could update your version with ​devtools::install_github("statOmics/stageR") and check if the error still occurs. Would you mind sharing (some of) your dat ...
written 7 months ago by Koen Van den Berge170
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Comment: C: simultaneous testing in DESeq2
... Thank you, Michael. However your response tests every hypothesis separately. I am rather interested in testing all three hypotheses simultaneously in an F-test like fashion, checking if any of the three are false with one omnibus test, rather than performing every test separately. ...
written 2.4 years ago by Koen Van den Berge170

Latest awards to Koen Van den Berge

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