User: Koen Van den Berge

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170
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Location:
Ghent University, Belgium
Last seen:
4 months, 1 week ago
Joined:
5 years, 5 months ago
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k***********@gmail.com

Posts by Koen Van den Berge

<prev • 34 results • page 1 of 4 • next >
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Answer: A: stageR with input from DRIMSeq
... Hi Sophia, The message about the removal of NA p-values is simply there for your information to check how many features have been removed prior to the analysis. Note that, even though you set `allowNA=TRUE`, nothing can be said about NA p-values, so they must be removed. Hence you can safely contin ...
written 4 months 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 5 months 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 5 months 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 5 months 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 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
... 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 11 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 11 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 12 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 12 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 12 months ago by Koen Van den Berge170

Latest awards to Koen Van den Berge

Popular Question 8 months ago, created a question with more than 1,000 views. For LIMMA similarity of contrast matrix, F test and topTable
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
Scholar 8 months ago, created an answer that has been accepted. For A: Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
Scholar 8 months ago, created an answer that has been accepted. For A: stageR NA in getAdjustedPValues() (method=dtu)
Popular Question 8 months ago, created a question with more than 1,000 views. For Hisat2 vs featureCounts summary statistics
Popular Question 2.1 years ago, created a question with more than 1,000 views. For convert S4 DataFrame of Rle objects to sparse matrix
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Hisat2 vs featureCounts summary statistics
Popular Question 3.3 years ago, created a question with more than 1,000 views. For convert S4 DataFrame of Rle objects to sparse matrix
Popular Question 3.3 years ago, created a question with more than 1,000 views. For EdgeR LogCpm and LogFC values calculation

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