User: Oskar

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Oskar40
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Posts by Oskar

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Comment: A: Error when using lfcShrink and contrast argument in DESeq2
... Hi Michael - I used "dots" instead underscores and it works. Thank you very much indeed. ...
written 9 weeks ago by Oskar40
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Error when using lfcShrink and contrast argument in DESeq2
... Hi everyone - I'm running a Differential Expression analysis via DESeq2 (DESeq2_1.16.1) . I have three levels in the conditions (SNP_A, SNP_B, and control), and I set as reference the "control" level. Each condition has three biological replicates. Then I ran this: dds <- DESeqDataSet(se, des ...
deseq2 lfcshrink written 9 weeks ago by Oskar40
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Answer: A: readCufflinks problem with extdata
... Many thanks for all those answers. Here I copy and paste how I get this package working in R v. 3.3.3 (Windows users) source("https://bioconductor.org/biocLite.R") biocLite() ##### To install old version of packages: install.packages("devtools") require(devtools) install_version("RSQLite", versi ...
written 3 months ago by Oskar40
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Answer: A: readCufflinks problem with extdata
... Hi - I also have exactly the same issue. Not sure what is going on; but when I re-run an analysis (previously done with an old version) it turn out with the outcome posted by biakemi. Here is the output. CuffSet instance with: 0 samples 0 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing ...
written 3 months ago by Oskar40

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