MaasLin2 Error Normalization

[sghos...@g.ucla.edu]

Hi there,

Is there a way to run the script in Rstudio? I tried with source("Maaslin2.R")

and getting following error:

ft_data <- Maaslin2(data21_Day,metadata21,output = "G:/mibiome" )

[1] "Warning: Deleting existing log file: G:/Liesbeth_mibiome/maaslin2.log"

2019-04-17 10:08:02 INFO::Writing function arguments to log file

2019-04-17 10:08:02 INFO::Verifying options selected are valid

2019-04-17 10:08:02 INFO::Determining format of input files

2019-04-17 10:08:02 INFO::Input format is data samples as rows and metadata samples as rows

2019-04-17 10:08:02 INFO::Formula for fixed effects: expr ~  group + Sex + DOL + DOL.group + Coll + Sex.Coll + DOL.gr.sex + DOL.gr.sex.coll

2019-04-17 10:08:02 INFO::Filter data based on min abundance and min prevalence

2019-04-17 10:08:02 INFO::Total samples in data: 78

2019-04-17 10:08:02 INFO::Min samples required with min abundance for a feature not to be filtered: 7.800000

2019-04-17 10:08:02 INFO::Total filtered features: 0

2019-04-17 10:08:02 INFO::Filtered feature names:

2019-04-17 10:08:02 INFO::Applying z-score to standardize continuous metadata

2019-04-17 10:08:02 INFO::Running selected normalization method: TSS

Error in normalizeFeatures(filtered_data, normalization = normalization) : 

  could not find function "normalizeFeatures"

can somebody please help me.

thanks

[rachael horne]

Hi,

You have to run the utility script as well as maaslin2.R. I attached it here. Also may want to make sure you have all the dependencies installed and loaded.

Best,

R