User: Frederik Ziebell

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EMBL Heidelberg
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http://www.huber.embl.de/
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Posts by Frederik Ziebell

<prev • 6 results • page 1 of 1 • next >
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Comment: A: DESeq2: Poor dispersion fit, even when a local or custom fit is used
... Hi Mike, indeed there are batch effects in the data. The way samples are processed is that 48 samples are always multiplexed together. So for these samples, library prep is performed, followed by sequencing and the combination of both is encoded as a "run". Here is a PCA of the vst-transformed coun ...
written 2 days ago by Frederik Ziebell0
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DESeq2: Poor dispersion fit, even when a local or custom fit is used
... I have a RNASeq data set with ~650 samples. When I run DESeq2, I get a very poor fit of the mean-dispersion trend: Here is also a plot of the original trend (without final dispersion estimates), and color coded the number of dispersion iterations: This is the output of DESeq: ​In DESeqDataSe ...
deseq2 dispersion written 3 days ago by Frederik Ziebell0
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Comment: A: rlog transformation producing outliers with very high log-transformed counts
... Hi Mike, thank you for your explanations. The reason I like to use rlog() over vst() is that it achieves almost equal within-sample distributions of counts across all samples, which may be connected to the size factor issue you were mentioning. Do you see potential future improvements of rlog() usi ...
written 11 weeks ago by Frederik Ziebell0
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rlog transformation producing outliers with very high log-transformed counts
... I have a data set in which the rlog transformation produces in one condition a few genes with very high log-transformed counts. Here is a mimimal example (the real data set has more gene but the same problems): library("DESeq2") library("tidyverse") # load data load(url("https://github.com/freder ...
deseq2 rlog written 11 weeks ago by Frederik Ziebell0
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Answer: A: Combine multiple sashimis stretching over the same intron
... I figured out the problem. It was not the missing sashimiFilterTolerance argument (which I used already), but the introns specified in the sashimiFilter argument. It contained the same intron multiple times and I suppose GViz draws a sashimi for each specified intron, if there are reads stretching ...
written 3 months ago by Frederik Ziebell0
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Combine multiple sashimis stretching over the same intron
... Visualizing my RNAseq data, I find many instances of multiple sashimis stretching over the same inton, see for example: https://i.imgur.com/rEK7bQM.png Is this a bug? If not, is there a way to combine those into one sashimi?       ...
gviz sashimi plots written 3 months ago by Frederik Ziebell0

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