User: anton.kratz

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anton.kratz40
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40
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United States, San Diego, UCSD
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1 month, 1 week ago
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Posts by anton.kratz

<prev • 20 results • page 1 of 2 • next >
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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 10 weeks ago by anton.kratz40
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6 follow
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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 10 weeks ago by anton.kratz40 • updated 10 weeks 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 6 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 9 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 9 months ago by anton.kratz40 • updated 9 months ago by Michael Love17k
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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 9 months ago by anton.kratz40
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is it necessary / recommended to separate samples when doing diff. exp. with DESeq2?
... I have biological states called sample1, sample2 and negative control (NC) in duplicate. They are all from the same sequencing run. I wrote R code using DESeq2 which generates all pairwise comparisons, i.e. sample1 vs NC, sample2 vs NC, sample1 vs sample2. I have all raw reads in a file expr_table ...
deseq2 written 9 months ago by anton.kratz40 • updated 9 months ago by Michael Love17k
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metagene: paired-end bam as input
... Regarding the metagene package (http://www.bioconductor.org/packages/release/bioc/html/metagene.html). I am using paired-end bam files as input. The plots which I generate with metagene look reasonable, but I am wondering what exactly is plotted. Does metagene consider the first base of each mate, ...
metagene written 18 months ago by anton.kratz40 • updated 18 months ago by Charles Joly Beauparlant160
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metagene: moving the legend
... Regarding the metagene package (http://www.bioconductor.org/packages/release/bioc/html/metagene.html). Can I move the legend of the final plot to a different position? At the moment I am using the plot command like this: mg$plot(title = "test metagene plot") The legend then appears on the right ...
metagene written 18 months ago by anton.kratz40 • updated 18 months ago by Charles Joly Beauparlant160
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metagene: strand orientation of plot?
... I am using the metagene package (http://www.bioconductor.org/packages/release/bioc/html/metagene.html) by Charles Joly Beauparlant and others. I would like to know if the plot considers strand orientation or not. I.e. the genomic regions used as input might be on the plus or on the minus strand. Now ...
metagene written 18 months ago by anton.kratz40 • updated 18 months ago by Charles Joly Beauparlant160

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