-
老师好，我想使用自带的mp_plot_abundance对自己的数据进行可视化。我有一份tax数据和一份otu数据，将它们转换为phyloseq格式后，使用as.MPSE()进行转换，可是出现了报错提示：**Warning message:
The taxonomy class can not be converted to treedata class. Please
check form…
-
Hi!
Im trying to use burrito to analyze a dataset obtained with picrust2; when I try the most simple way to use Burrito with Taxonomic abundances: (OTU abund table), Custom taxon IDs with no hierac…
-
Hello! This is my first time using FUNGuild and I would like to know more about the ASV input table. Should I use read counts or relative abundances? I am trying to check this by opening the example O…
-
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 imp…
-
An unusual behavior from the default `pick_open_reference_otus.py` pipeline. Samples which are seen with low counts after `min_count` filtering can then be preserved in the final biom table even thoug…
-
Hi,
I would like to create some barplots with calculated values of an absolute abundance.
I have a Phyloseq object with relative abundance values, created like this from a standard count table of il…
-
Background: I have used bacterial spicke as an internal standard. Using that I have adjusted the raw data.
Now, I have data which is mix of both integer and non-integer number.
What I need is …
zmt11 updated
6 years ago
-
Hi, im interested in trying out your tool, but i get the following error when trying to run the example from the mms vignette:
I get the following error at `out = fixed(f)$dist`:
```
Error in fixed…
-
The OTU+contextual download is slow. It gets about 200KB/s in production.
In the development environment, `top` shows that the python process is probably the bottleneck, as it hovers close to 100% …
-
Hi guys
I rarefy my otu table to 4100 sample size and after rarefying to even depths, 1296 OTUs were removed because they are no longer present in any sample after random subsampling. Now I am wonder…