User: gaio.transposon

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Posts by gaio.transposon

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differential abundance with Voom - blocking per subject - making contrasts
... Hi everyone, I am using Voom to test a few hypotheses in my data. NB, my data is metagenomic reads of gut microbiome communities (rather than RNA where Voom is more commonly used for). We have a very large amount of data ( 126 pigs; 6 cohorts; each pig sampled about 6-8 times throughout a 6 weeks ...
differential abundance limma voom written 6 months ago by gaio.transposon0
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Comment: C: Limma/edgeR or other for metagenomic (non-RNA) data?
... Thank you Fabio. I remember reading a paper that compared metagenomeseq to edgeR among others and metagenomeseq would not perform really well: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2386-y Did you use metegenomeseq when you had two groups to compare, each with => 2 tim ...
written 7 months ago by gaio.transposon0
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Comment: C: Limma time-course: how to apply differential contrast if time zero is considered
... Thank you Kevin, yes that post is indeed very similar to what I need to do. I have been fiddling with the code further and given that my data is slightly different I decided to post my concerns. Here, if you could please help: https://www.biostars.org/p/404977/ ...
written 7 months ago by gaio.transposon0
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Limma/edgeR or other for metagenomic (non-RNA) data?
... Hi everyone, I have been stuck a few days on this problem, so I thought I'd better ask. This is not just any edgeR question as the input data is different than usual (non-RNA). So if anyone knows of a better tool to run this analysis please tell me, otherwise just assume the data is RNA counts data ...
metagenomics paired data edger voom written 7 months ago by gaio.transposon0 • updated 7 months ago by Fabio Marroni2.5k
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Comment: C: Limma time-course: how to apply differential contrast if time zero is considered
... Hi Kevin, I am after the exact same answer. Given that I would have enough samples, would the contrast mentioned above `(Dif_6hr=(Cld _6hr- Cld _1hr)-(Amb_6hr-Amb_1hr))` be correct? This is an example of my own dataframe: df <- data.frame(timepoint = rep_len(0:1, length.out=16), ...
written 7 months ago by gaio.transposon0 • updated 7 months ago by Kevin Blighe60k

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