MicrobiomeStat

MicrobiomeStat copied to clipboard

Datatype of feature.tab not matrix after normalization

10

**Describe the Bug** When I use mStat_normalize_data() with the Rarefy-TSS method, the mStat_validate_data() function no longer passes because it doesn't recognize feature.tab as a matrix (Rule 5). When I don't...

pkirti33

Error in midpoint(data.obj$tree) : could not find function "midpoint"

2

Dear developer, Congratulations for this great tool. I have a problem while trying to convert my phyloseq object to microbiomeStat object. It seems it does not found midpoint function. I...

nutrimol

mStat_generate_report_single(): error in linda() call

1

`mStat_generate_report_single()` fails due invalid call to `linda()` in `MicrobiomeStat_1.1.3`: ``` processing file: file10828c3bf4e.Rmd |........................ | 78% [taxa-test-execution] Quitting from lines 615-626 [taxa-test-execution] (file10828c3bf4e.Rmd) Error in `linda()`: ! unused arguments (feature.sig.level...

SciLiciumTheo

qiime2 style metadata import error

1

When importing a qiime2 style metadata file, the function mStat_import_qiime2_as_data_obj() does not remove the annotation row "q2:types" specifing the data type data.obj head(data.obj$meta.dat) sample.id barcode.sequence body.site year month day subject...

magicprotoss

Could not find function "mStat_convert_phyloseq_to_data_obj"

13

Hello, I am excited to use the MicrobioStat package in order to test for differences in alpha diversity accross timepoints. I have been working with phyloseq object so far and...

QGaelle

Problems with MicrobiomeStat.rdb

4

Dear Chen Yang, Thank You for creating the MicrobiomeStat tools. I would really like to process my data using your package and generate_beta_change_test_long() , but I am facing a problem...

kuzmpa

generate_beta_ordination_single: meta_tab not found

1

Hi, From looking at the code of generate_beta_ordination_single, it looks like you forgot to define 'meta_tab' in the function before calling it.

sdoms

Error: number of observations (=44) <= number of random effects (=44) for term (1 + time | subject)

7

First of all thank you for a very useful package! It would be great if you can give some clarifications regarding the following error: Error in linda: Error in fun(i):...

AlexanderUm

Error when running generate_beta_trend_test_long() function

4

Dear Chen Yang, Thank you for your work and your time in trying to answer all the questions users are aiming at you. I know you are very busy and...

QGaelle

Format time.var in generate_alpha_trend_test_long() function

10

Dear Chen Yang, I have a question regarding the use of the generate_alpha_trend_test_long() function. I am working on the microbiome communities of three coral species. Individual colonies of each species...

QGaelle