Hi Dan Knights, what other learning sources (essential books, lectures, papers) would you suggest for techniques/pipelines in studying microbiome? Especially for statistical testing. 18:00 we use absolute abundances with "-a", not relative :)
Hi, thanks for providing these videos. I have a question. I used spearman correlations to test associations between levels of stress and RELATIVE abundances of certain microbes. Many were significantly associated, however, the microbiome data were not normally distributed so I conducted Negative Binomial regressions as a follow-up. Now, nothing is significant and I think it's because I switched from using relative abundances in the spearman correlations to using absolute abundances for the negative binomial regressions. In which types of regressions can I continue to use RELATIVE abundances instead of absolute? Thanks!! Any tips would be EXTREMELY appreciated! p.s. I did not use the same package as you use here to run the Negative Binomial regressions. Could that be the problem?
Another question: 18:21. If we are operating on counts, then "pruning" or "subsetting" out genus table with ">= .1 " will not give us genuses with abundance greater than 10%. We're operating on counts right now, and coun't could be unrarefied - i.e. different number of total count for each sample.
Hello! Thank you for your tutorials. I have been working through them to understand statistical analyses for microbiomes better. I am now at the section of GLM. Whn doing analyses with edgeR package, do I have to run the wrapper script every single time? I thought that could be the problem, since removing rare taxa with 'genus.a[,colMeans(genus.a > 0) >= .1]' (Error in colMeans(genus.a > 0) : 'x' must be an array of at least two dimensions) and running 'colnames(genus.a)
Very good videos, Thank you so much. I am looking for the analysis PERMANOVA which has been used in last papers of microbiota (animal). I need to understand concepts, when and how to use it, then how to run it. Could you please explain about that? Best regards from Chile.
very useful, straightforward course, found it helpful even though I used mothur for already 2 year
Hi Dan Knights,
what other learning sources (essential books, lectures, papers) would you suggest for techniques/pipelines in studying microbiome? Especially for statistical testing.
18:00 we use absolute abundances with "-a", not relative :)
Hi, thanks for providing these videos. I have a question. I used spearman correlations to test associations between levels of stress and RELATIVE abundances of certain microbes. Many were significantly associated, however, the microbiome data were not normally distributed so I conducted Negative Binomial regressions as a follow-up. Now, nothing is significant and I think it's because I switched from using relative abundances in the spearman correlations to using absolute abundances for the negative binomial regressions. In which types of regressions can I continue to use RELATIVE abundances instead of absolute? Thanks!! Any tips would be EXTREMELY appreciated!
p.s. I did not use the same package as you use here to run the Negative Binomial regressions. Could that be the problem?
Another question: 18:21.
If we are operating on counts, then "pruning" or "subsetting" out genus table with ">= .1 " will not give us genuses with abundance greater than 10%. We're operating on counts right now, and coun't could be unrarefied - i.e. different number of total count for each sample.
Hello!
Thank you for your tutorials. I have been working through them to understand statistical analyses for microbiomes better.
I am now at the section of GLM. Whn doing analyses with edgeR package, do I have to run the wrapper script every single time?
I thought that could be the problem, since removing rare taxa with 'genus.a[,colMeans(genus.a > 0) >= .1]'
(Error in colMeans(genus.a > 0) :
'x' must be an array of at least two dimensions)
and running 'colnames(genus.a)
18:10 it's absolute abundance, not relative abundance.
Thanks for another excellent lecture. One question, what is a confounding variable?
Very good videos, Thank you so much. I am looking for the analysis PERMANOVA which has been used in last papers of microbiota (animal). I need to understand concepts, when and how to use it, then how to run it. Could you please explain about that? Best regards from Chile.