User: Koen Van den Berge

Reputation:
90
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Trusted
Location:
Ghent University, Belgium
Last seen:
2 months, 3 weeks ago
Joined:
3 years, 9 months ago
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k***********@gmail.com

Posts by Koen Van den Berge

<prev • 24 results • page 1 of 3 • next >
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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 14 months ago by Koen Van den Berge90
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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 14 months ago by Koen Van den Berge90 • updated 14 months ago by Michael Love14k
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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 15 months ago by Koen Van den Berge90 • updated 15 months ago by Gordon Smyth32k
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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 18 months ago by Koen Van den Berge90
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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 18 months ago by Koen Van den Berge90
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Hisat2 vs featureCounts summary statistics
... I am processing paired-end RNA-Seq data. I map them using Hisat2.0.3.Next I convert SAM files to BAM, sort and index the BAM file using samtools 1.3. I subsequently use the sorted BAM files to aggregate mapped reads based on annotation using featureCounts (Rsubread package v1.20.6). After mapping t ...
featurecounts rna-seq mapping hisat2 written 18 months ago by Koen Van den Berge90 • updated 18 months ago by Wei Shi2.7k
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Comment: C: bounded trended dispersion edgeR
... Dear Aaron I have uploaded an example just to make things clear. You can find it at https://www.dropbox.com/s/7kl3e9fsjbwn1wl/bcvExample.pdf?dl=0 . Please let me know if the function will be updated in order to cope with the weights. Thank you in advance. ...
written 20 months ago by Koen Van den Berge90
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Comment: C: bounded trended dispersion edgeR
... Dear Aaron, thank you for the answer. What I meant by bounded is that the trended dispersion trend cannot exceed a BCV of 2 in the estimateGLMTrendedDisp function, at which it will asymptote when it actually should be higher. Would the only modification for a weighted estimateDisp function be to ad ...
written 20 months ago by Koen Van den Berge90
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bounded trended dispersion edgeR
... In edgeR, one usually estimates a common, trended and tag wise dispersion in order to estimate the mean-variance trend over all genes. I have noisy data with large BCVs. It is actually single-cell RNA-seq, and just for comparison, I would like to analyse it with edgeR. However, the common, trended ...
edger written 20 months ago by Koen Van den Berge90 • updated 20 months ago by Aaron Lun17k
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Comment: C: edgeR no residual degrees of freedom for a specific row of numbers in dispCoxRei
... Thank you Yunshun and Aaron, this cleared things up. Indeed, it works when using the estimateDisp rather than the estimateGLMTagwisdeDisp function, this was a great help. ...
written 22 months ago by Koen Van den Berge90

Latest awards to Koen Van den Berge

Popular Question 20 months ago, created a question with more than 1,000 views. For convert S4 DataFrame of Rle objects to sparse matrix
Popular Question 20 months ago, created a question with more than 1,000 views. For EdgeR LogCpm and LogFC values calculation

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