Moderator: Philipp Bayer

gravatar for Philipp Bayer
Philipp Bayer5.8k
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PhilippBayer
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Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org

Posts by Philipp Bayer

<prev • 467 results • page 1 of 47 • next >
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Comment: C: EIGENSOFT: CONVERTF ignoring samples
... If I remember correctly, that column is reserved for phenotypes, which are not used in the PCA ...
written 9 days ago by Philipp Bayer5.8k
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Answer: A: geneontology.org GO annotations no longer present
... Could you maybe have used amigo**2**? http://amigo2.geneontology.org/amigo/search/annotation has 17,511 GO terms for *T. thermophila* ...
written 9 days ago by Philipp Bayer5.8k
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Comment: C: Why use LASSO / elastic net in survival regression?
... You will probably get a better answer to your stats question on [Cross Validated][1] [1]: https://stats.stackexchange.com/ ...
written 16 days ago by Philipp Bayer5.8k
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Answer: A: total beginner trying to learn about quality control
... Would [MultiQC][1] be fine? However, it makes a new HTML file summarising all input reports, I don't think it can make a CSV [1]: https://multiqc.info/ ...
written 5 weeks ago by Philipp Bayer5.8k
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Comment: C: How to run sleuth in single run mode?
... The way I understand that thread, `sleuth_live`, **not** `sleuth` now has a single library running mode - `sleuth_live` is the web server for explanatory data analysis, it doesn't do differential expression ...
written 5 weeks ago by Philipp Bayer5.8k
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Comment: C: How to solve ufasta error while running MaSuRCA
... Have you tried recompiling (rerunning install.sh)? Looks like ufasta is looking for GLIBC libraries that aren't there ...
written 6 weeks ago by Philipp Bayer5.8k
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Comment: C: FarmCPU - how to explain the reported 'effect'?
... Thank you Kevin! Yes, the coefficient makes much more sense - I'm using MVP currently which doesn't let me set `Major.allele.zero`, I will have to ask the authors! ...
written 6 weeks ago by Philipp Bayer5.8k
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FarmCPU - how to explain the reported 'effect'?
... When you run a GWAS using FarmCPU via GAPIT or MVP, you get an 'effect' reported per SNP (a number somewhere around -1 to +1, with a bunch of outliers). I've looked at the papers and the GAPIT forum but I'm not understanding what the effect itself reports. Is it the effect of the minor allele? The ...
gwas written 6 weeks ago by Philipp Bayer5.8k
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Answer: A: Getting loadings of components from pcaMethods
... Wouldn't you just need to transpose your input table while keeping names intact? tx = setNames(data.frame(t(x[,-1])), x[,1]) loadings(pca(tx, method="nipals", nPcs=2)) ...
written 6 weeks ago by Philipp Bayer5.8k
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Answer: A: How to add help function in a snakemake file
... Maybe [this older tutorial and its answers][1] can help you? [1]: https://www.biostars.org/p/220268/ ...
written 8 weeks ago by Philipp Bayer5.8k

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