User: anton.kratz

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anton.kratz40
Reputation:
40
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Location:
United States, San Diego, UCSD
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17 hours ago
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3 years, 1 month ago
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a**********@gmail.com

Posts by anton.kratz

<prev • 24 results • page 1 of 3 • next >
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No gene set have size > 10 ...
... I am using clusterProfiler to check whether a group of genes of interest is enriched in genes coming from a term from a custom ontology. I am following the outline provided by this article: "use clusterProfiler as an universal enrichment analysis tool", http://guangchuangyu.github.io/2015/05/use-clu ...
clusterprofiler gene ontology written 18 hours ago by anton.kratz40
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topGO: how to print GO descriptions only when using showSigOfNodes?
... I am using topGo following this outline https://datacatz.wordpress.com/2018/01/19/gene-set-enrichment-analysis-with-topgo-part-1/ At the end of my analysis, I visualize the result with showSigOfNodes: showSigOfNodes(GOdata, score(weight_fisher_result), useInfo = "all", sigForAll=FALSE, firstSigNo ...
topgo written 6 weeks ago by anton.kratz40
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Comment: C: Error: could not find function "godata"
... Thank you, yes, I could now make it work with R 3.4! (Could not install R 3.5 because this led to some package confusion loop). R version 3.2.3 is what comes with Ubuntu 16.04 LTS so I think a great number of people are using it. I am not contradicting you, just saying that although 3.2.3 might be ...
written 3 months ago by anton.kratz40
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Error: could not find function "godata"
... I am trying to use GOSemSim, code which run previously does not run anymore. It does not seem to fin the function godata, but why? Minimal reproducible example:   ​> library("GOSemSim") > library("org.Sc.sgd.db") > library("GO.db") > yeastGO <- godata('org.Sc.sgd.db', keytype = "ENSE ...
gosemsim written 3 months ago by anton.kratz40
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Comment: C: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
... Hi Guangchuang, great that the original author chimes in as well, I do not know how to update to 2.5.1, though (I am on Bioconductor version 3.6, R version 3.4.3). Another question. I was wondering about the exact way you are computing Resnik. In my understanding Resnik in the original 1996, 1999 p ...
written 8 months ago by anton.kratz40
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Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
... Using the GOSemSim package, I am trying to generate a data frame which contains the semantic similarity between any two gene identifiers in yeast, like this (minimal, reproducible example): library("GOSemSim") yeastGO <- godata('org.Sc.sgd.db', keytype = "ENSEMBL", ont="BP", computeIC = TRUE) ge ...
gosemsim gene ontology written 8 months ago by anton.kratz40 • updated 8 months ago by ellascottgm0
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[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
... When running the sva function, I get an error "Error in density.default(x, adjust = adj) : 'x' contains missing values". I have a data frame with raw RNA-seq counts with sample names in columns and gene names in rows, and another data frame describing the condition of each sample. There is only one ...
sva written 12 months ago by anton.kratz40
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Comment: C: all pairwise comparisons, some genes can have zero counts everywhere in a given
... Thank you. I was not using lfcShrink,  but now I am and this fixed my issue - I am on DESeq2 v 1.16.1 and was simply not aware that lfcShrink is not called implicitly anymore, now I am calling explicitly. ...
written 15 months ago by anton.kratz40
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all pairwise comparisons, some genes can have zero counts everywhere in a given comparison
... I have 12 different biological states in triplicate and do all pairwise differential expression tests between these samples with DESeq2. There can be any combination of two given states such that specific clusters (genes) have absolutely zero counts in all three replicates each, for this particular ...
deseq2 written 15 months ago by anton.kratz40 • updated 15 months ago by Michael Love19k
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Comment: C: is it necessary / recommended to separate samples when doing diff. exp. with DES
... Thank you Michael! Indeed it is there at https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#if-i-have-multiple-groups-should-i-run-all-together-or-split-into-pairs-of-groups ...
written 15 months ago by anton.kratz40

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Popular Question 15 months ago, created a question with more than 1,000 views. For how can I install packages in docker/R/bioconductor so that they persist?
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