User: Koen Van den Berge

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120
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Ghent University, Belgium
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4 years, 8 months ago
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Posts by Koen Van den Berge

<prev • 29 results • page 1 of 3 • next >
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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 8 weeks ago by Koen Van den Berge120
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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 8 weeks ago by Koen Van den Berge120
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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 weeks ago by Koen Van den Berge120
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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 weeks ago by Koen Van den Berge120
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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 weeks ago by Koen Van den Berge120
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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 2.1 years ago by Koen Van den Berge120
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simultaneous testing in DESeq2
... Suppose I am analysing a dataset with two timepoints, two conditions within every timepoint and three replicates for every time-treat combination. Furthermore suppose that the hypotheses of interest are (a) DE within timepoint1 (b) DE within timepoint2 (c) differential DE between timepoint1 and time ...
deseq2 written 2.1 years ago by Koen Van den Berge120 • updated 2.1 years ago by Michael Love19k
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variance-covariance matrix edgeR
... A relatively simple question. I wonder if it is possible to extract gene-wise variance covariance matrices of the GLM coefficients in edgeR. I would like to use it for non-standard multiple comparison procedures. Thank you.   ...
edger written 2.2 years ago by Koen Van den Berge120 • updated 2.2 years ago by Gordon Smyth35k
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Comment: C: Hisat2 vs featureCounts summary statistics
... Dear Wei, thanks again. I used featureCounts (Rsubread_1.20.6) with the following arguments: featureCounts ( f i l e s = bamFiles , annot . ext=”xxx.gff3”, isGTFAnnotationFile = TRUE, useMetaFeatures = TRUE, isPairedEnd=TRUE, requireBothEndsMapped = TRUE, GTF . featureType = ”CDS” , GTF. attrType ...
written 2.4 years ago by Koen Van den Berge120
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Comment: C: Hisat2 vs featureCounts summary statistics
... Thank you for your reply, Wei. So the larger number of fragments reported by featureCounts may be the result of multi-mapping reads? However, similar, the number of counted fragments is higher than the number of concordantly mapped reads (exactly one time as in the example above) for some of the s ...
written 2.4 years ago by Koen Van den Berge120

Latest awards to Koen Van den Berge

Popular Question 16 months ago, created a question with more than 1,000 views. For Hisat2 vs featureCounts summary statistics
Popular Question 16 months ago, created a question with more than 1,000 views. For convert S4 DataFrame of Rle objects to sparse matrix
Popular Question 2.6 years ago, created a question with more than 1,000 views. For convert S4 DataFrame of Rle objects to sparse matrix
Popular Question 2.6 years ago, created a question with more than 1,000 views. For EdgeR LogCpm and LogFC values calculation

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