User: arne.smits

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arne.smits60
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Posts by arne.smits

<prev • 9 results • page 1 of 1 • next >
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Answer: A: DEP package: error in plot_heatmap
... Dear robert.arsie, A fix is available in the new version of DEP (version 1.6.1). # Update Bioconductor packages: BiocManager::install() Best, Arne ...
written 3 months ago by arne.smits60
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Comment: C: DEP package: error in plot_heatmap
... Dear robert.arsie, Thank you for pointing out the bug. I am working on it and will let you know once a fix is available. Best, Arne ...
written 4 months ago by arne.smits60
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Comment: C: Error: se does not inherit from class SummarizedExperiment
... deleted entry: double entry ...
written 4 months ago by arne.smits60
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Comment: C: Error: se does not inherit from class SummarizedExperiment
... Hi Wuschel, Please provide more information, so that I have a working example of the error. The error states that one of your input objects that should be of the class SummarizedExperiment, which is the object class that the DEP package is working with, is not a SummarizedExperiment. Best, Arne ...
written 4 months ago by arne.smits60
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Answer: A: Clarification of results tables in DEP
... deleted entry: double entry ...
written 4 months ago by arne.smits60
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Answer: A: Clarification of results tables in DEP
... Daar António, CI.L and CI.R depict the confidence interval of the logFC. These values are generated using limma. In your example, this would be the confidence interval for the logFC of Ubi4vsCtrl. Please have a look at this other question for detailed answers on the [interpretation of confidence in ...
written 4 months ago by arne.smits60
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Comment: C: Clarification of results tables in DEP
... deleted - wrong spot ...
written 4 months ago by arne.smits60
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Comment: C: Imputation method selection (mass spectrometry) bimodal distribution
... I completely agree with Laurent. ...
written 2.0 years ago by arne.smits60
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Answer: A: DEP: Grouping Samples for missing value imputation
... The data is stored in a SummarizedExperiment object in DEP. Therefore, we need a small workaround to be able to use Laurent's solution. DEP offers the function se2msn to easily turn a SummarizedExperiment into an MSnSet. Next, we use the exprs and impute functions from MSnbase and eventually store t ...
written 2.0 years ago by arne.smits60

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Scholar 4 months ago, created an answer that has been accepted. For A: Clarification of results tables in DEP

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