User: tkapell

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tkapell0
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Posts by tkapell

<prev • 21 results • page 1 of 3 • next >
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Installation of r2excel package
... Hi, I m trying to install r2excel from the kassambara github, but I get the following error. Can anyone help? Installing package into ‘C:/Users/Theo/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) * installing *source* package 'r2excel' ... ** R ** byte-compile and prepa ...
packages github written 8 weeks ago by tkapell0 • updated 8 weeks ago by Gordon Smyth36k
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Comment: C: DESeq2: removal of duplicated genes during statistical analysis
... I did a gene differential expression analysis using transcriptome levels therefore my count table has transcript version IDs (e.g. ENSG00000000003.14). When I convert those to ensembl IDs (e.g. ENSG00000000003), there are about 30 genes which share the same ensembl ID because they are paralogs in th ...
written 3 months ago by tkapell0
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DESeq2: removal of duplicated genes during statistical analysis
... Hi all, in my latest analysis with the DESeq2 package, I noticed that I had a few paralog genes (~30) which shared the same statistics and ensembl ID. I can use only the unique genes, but I was wondering whether it would be more appropriate to remove the duplicated genes before the statistical anal ...
deseq2 ensembl gene symbol written 3 months ago by tkapell0 • updated 3 months ago by Michael Love22k
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Comment: C: GSEA using TFs as the gene set
... Thank you lhuang7. May I ask what is the difference between the two? ...
written 4 months ago by tkapell0
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GSEA using TFs as the gene set
... Hi all,     I have a DE gene dataset and I would like to know which TFs have binding sites at the promoters of these genes. I found a list of 615 human TFs on the GSEA website with the genes they bind to, but my DE gene list is too large to manually test. I then thought to create custom GO terms us ...
gsea transcription factor binding site enrichment analysis written 4 months ago by tkapell0 • updated 4 months ago by lhuang730
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Comment: C: How are the shrunk result data used in DESeq2?
... Thanks for the reply. I now understand why I should use lfcShrink, but wonder whether one can pass all the results arguments in this function as well, e.g. cooksCutoff, independentFiltering, altHypothesis, filterFun. Does lfcShrink run results internally or should I have to run results first and the ...
written 11 months ago by tkapell0
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How are the shrunk result data used in DESeq2?
... I am a bit confused with the "lfcshrink" function in DESeq2. I would assume that one would want to use the shrunk result table in subsequent DE gene analysis, but the DESeq2 manual suggests that lfc shrinkage is only used for data visualisation. Could someone clarify how "results" and "lfcshrink" ar ...
deseq2 lfcshrink written 11 months ago by tkapell0 • updated 11 months ago by Michael Love22k
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Comment: C: How to get DE relative to a fold-change threshold in single factor experiments
... Ok all clear then. Thanks ...
written 12 months ago by tkapell0
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Comment: C: How to get DE relative to a fold-change threshold in single factor experiments
... Yes, that was from the link you posted above. You said that glmQLFit approximations fail with small counts and large dispersions. Can you then elaborate when you would switch to glmFit based on this? ...
written 12 months ago by tkapell0
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Comment: C: How to get DE relative to a fold-change threshold in single factor experiments
... "In summary, while both of the methods will work for your data set, the QL F-test is probably the better choice. There are some situations where the QL F-test doesn't work well - for example, if you don't have replicates, you'd have to supply a fixed dispersion, which defeats the whole point of mode ...
written 12 months ago by tkapell0

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