User: Stefan Dentro

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Posts by Stefan Dentro

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Comment: C: DEXSeq many exons marked as not testable
... Ah that worked, cheers! On Thu, Sep 20, 2012 at 4:34 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > On Thu, Sep 20, 2012 at 8:52 AM, Stefan Dentro wrote: > > That is great! Thank you for the quick response! > > > > 1.3.20 is not in biocLit ...
written 6.2 years ago by Stefan Dentro70
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Comment: C: DEXSeq many exons marked as not testable
... That is great! Thank you for the quick response! 1.3.20 is not in biocLite yet and I cannot find an SVN repository to fetch it from. How can I obtain it? Stefan On Thu, Sep 20, 2012 at 12:20 PM, Alejandro Reyes wrote: > Dear Stefan Dentro, > > Thank you very much for sending me your Exo ...
written 6.2 years ago by Stefan Dentro70
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Comment: C: DEXSeq many exons marked as not testable
... Perhaps a clue: If I add a second gene to the small dataset I get the following error message: > genes[1] "ENSG00000009780" "ENSG00000034533" ... > cds = estimateDispersions(cds, minCount=2, maxExon=90) Dispersion estimation. (Progress report: one dot per 100 genes)Error in which(sapply(m ...
written 6.2 years ago by Stefan Dentro70
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Comment: C: DEXSeq many exons marked as not testable
... Hi Alejandro, I just reran the code with only ENSG00000009780 in the dataset. The odd thing is that this time it worked perfectly. Regards, Stefan ## Only ENSG00000009780 > counts(cds) sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8 sample9 sample10 sample11 sample12 sa ...
written 6.2 years ago by Stefan Dentro70
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DEXSeq many exons marked as not testable
... Hello, I'm using DEXSeq to obtain differentially expressed exons between my 15 samples and 8 controls. But for some reason most exons are not testable and are not assigned a p-value. Do you know what I'm doing wrong? First I've created a conservative list of exons per gene in the human genome thro ...
dexseq written 6.2 years ago by Stefan Dentro70 • updated 6.2 years ago by Stefan Dentro10
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Comment: C: How to combine VCF-class and data.frame with annotations
... That works well! vcf.df = as(elementMetadata(vcf), "DataFrame") anno.df = as(anno, "DataFrame") elementMetadata(vcf) = cbind(vcf.df, anno.df) Cheers! Stefan On Wed, Aug 29, 2012 at 3:24 PM, Vincent Carey wrote: > > > On Wed, Aug 29, 2012 at 10:16 AM, Stefan Dentro wrote: > >> ...
written 6.2 years ago by Stefan Dentro70
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How to combine VCF-class and data.frame with annotations
... Hello, I'm trying to read in a VCF file containing mutation information from one sample, annotate it with Ensembl gene and GO information and then plot using ggbio. But I keep running into the problem of how to combine all information in one single GRange object. So I've got a VCF-class object and ...
go annotate convert ggbio written 6.2 years ago by Stefan Dentro70 • updated 6.2 years ago by Vincent J. Carey, Jr.6.2k

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Popular Question 6.2 years ago, created a question with more than 1,000 views. For How to combine VCF-class and data.frame with annotations

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