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Search: Posts Made By: sarah_27_m
Forum: Bioinformatics 01-11-2017, 08:53 AM
Replies: 1
Views: 1,573
Posted By sarah_27_m
Just in case anyone else has this problem, there...

Just in case anyone else has this problem, there is a pretty simple fix that worked for me (took me a while to find!!!!)

You can agglomerate taxa of the same type, so for me I did this:

(x1 <-...
Forum: Bioinformatics 01-11-2017, 04:46 AM
Replies: 1
Views: 1,318
Posted By sarah_27_m
The answer to part of my question, this...

The answer to part of my question, this demonstrates that microbiome count data from amplicon sequencing experiments can be treated with the same procedures as for differential expression data from...
Forum: Bioinformatics 01-10-2017, 08:15 AM
Replies: 1
Views: 1,573
Posted By sarah_27_m
Red face Using DeSeq2 in R or Qiime to examine taxonomic rank other than OTU level

Hello,

I am trying to follow the example given here https://github.com/joey711/phyloseq/issues/683, using DeSeq2 to examine differential abundance at Genus rather than OTU level, however When I...
Forum: Bioinformatics 01-06-2017, 05:31 AM
Replies: 1
Views: 1,318
Posted By sarah_27_m
Question Using DeSeq2 with 16s data, valid parameters

Hello,

I am trying to use DeSeq2 in R to analyse differential abundance between 16s samples at OTU level. However I am not sure if the code I am using is valid for what I want to do. Codes comes...
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