User: gil.hornung

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Posts by gil.hornung

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"Over-correction" in the size-factors of the DESeq2 package
... Hi, I have RNA-seq samples from yeast (~6000 genes), and there is very large variability in the total number of counts in each sample. In one of the samples I have a large number of genes with very low expression (949 genes with counts=0 and 3643 genes with counts<50). When I look at the size fa ...
normalization deseq2 rna-seq written 19 months ago by gil.hornung0
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Error when trying to load a gff3 with GenomicFeatures
... Hi, I downloaded the GFF file for S. cerevisiae from NCBI: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.gff.gz I'm trying to open the file with the following command: txdb <- makeTranscriptDbFromGFF("genomes/Saccharomyces_cerevisiae/GCF_000146045.2_R ...
genomicfeatures written 20 months ago by gil.hornung0 • updated 20 months ago by Mike Smith2.1k
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Comment: C: NA in padj in the DEXSeq package
... Only individual exons ...
written 22 months ago by gil.hornung0
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Answer: A: NA in padj in the DEXSeq package
... A related issue: I also seem to get NA in the coefficients of some genes, and the log2FoldChange. The counts of such cases are reasonable. Table of such cases are below, and image of one of these cases is attached   ...
written 22 months ago by gil.hornung0
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Answer: A: NA in padj in the DEXSeq package
... Dear Alejandro, Thank you for the fast reply. I suspected that it has something to do with the independent filtering, which I know from DESeq2. Your reply solved my problem.   Here is the sessionInfo: R version 3.1.1 (2014-07-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTY ...
written 22 months ago by gil.hornung0
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NA in padj in the DEXSeq package
... Hi, I'm trying to use DEXSeq on RNA-seq data. There is one gene I know is supposed to have differential exon usage, because a few of the exons were knocked-out. When I look at the data of this gene I see a beautiful plot that suggests differential splicing (as expected, see attached figure), and a ...
dexseq padj written 22 months ago by gil.hornung0

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