The bioBakery help forum

Running a melonnpan tutorial

Hello,

I wonder if you could give me help on running the melonnpan.predict.
I am trying to run the Melopann tutorial using the sample file provided here (https://bitbucket.org/biobakery/biobakery/wiki/melonnpan), but I always get this error “Error in melonnpan.predict(data_norm, weight.matrix = NULL) :
All measurements should be normalized to proportions.”
Any help?
Thanks,
Rui

Please see the code I used:
##Packages installed

devtools::install_version("GenABEL.data", version = "1.0.0", repos = "http://cran.us.r-project.org")

devtools::install_version("GenABEL", version = "1.8-0", repos = "http://cran.us.r-project.org")

## Installation of MelonnPan ##
devtools::install_github("biobakery/melonnpan")

#HTSSIP: analyzing high throughput sequence data from nucleotide stable isotope probing experiments, used to nomralize the data
install.packages("HTSSIP")

##Load packages

library("melonnpan")
library("optparse")
library("GenABEL")
library("HTSSIP")

1.Load the sample data - melonnpan.test.data.txt

data_test <- read.table(file.choose(), header = TRUE, sep = "\t", quote = "", row.names = 1)

2.Data normalized to proportions ranging between 0 and 1

data_norm <- tss(data_test, MARGIN = 1, na.rm = FALSE)

3.Verified that the sum of each row is equal to 1

apply(data_norm, 1, sum)

5. Run melonnpan_predict

metabolites <- melonnpan.predict(data_norm, weight.matrix = NULL)
head(metabolites)

I always got this error:
Error in melonnpan.predict(data_norm, weight.matrix = NULL) :
All measurements should be normalized to proportions.

I am assuming that this topic has been resolved through GitHub: https://github.com/biobakery/melonnpan/issues?q=is%3Aissue+is%3Aclosed. Please let me know if not.