Moderator: Philipp Bayer
Philipp Bayer ♦ 5.8k
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Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org
Posts by Philipp Bayer
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... If I remember correctly, that column is reserved for phenotypes, which are not used in the PCA ...
written 9 days ago by
Philipp Bayer ♦ 5.8k
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... 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 Bayer ♦ 5.8k
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... 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 Bayer ♦ 5.8k
2
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... 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 Bayer ♦ 5.8k
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... 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 Bayer ♦ 5.8k
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... 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 Bayer ♦ 5.8k
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... 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 Bayer ♦ 5.8k
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... 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 ...
written 6 weeks ago by
Philipp Bayer ♦ 5.8k
0
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1
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102
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... 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 Bayer ♦ 5.8k
1
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... Maybe [this older tutorial and its answers][1] can help you?
[1]: https://www.biostars.org/p/220268/ ...
written 8 weeks ago by
Philipp Bayer ♦ 5.8k
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