Error when running mbImpute

[zifanzhu]

Hello, mbImpute developers,

I read your mbImpute manuscript on bioRxiv recently. I really liked the idea and would like to give it a try on my datasets. However I kept getting the following error when running the imputation:

This is the code I'm using:
a_imp <- mbImpute(condition = a_meta_num, otu_tab = otu_tab).

The otu_tab and a_meta_num I used is attached below in RDS format ('data.zip'). The entry of the otu_tab is defined as raw_counts divided by total_counts_in_the_sample, which is similar to the one presented in your manuscript except that it doesn't multiply by 10^6.
data.zip

Could you please help me look into this? Thanks in advance!

Also, there's a small typo in README. It should be
install.packages("glmnet")
instead of
install.pacakges("glmnet").

Best,
Zifan

[ruochenj]

Hi Zifan,

Since we are using a gamma normal mixture model to identify the zero counts or low values we will impute on, the smallest number cannot be 0. It should be a small positive number instead. You can use the current data scaled by a scalar (e.g. the median of the total counts in each sample) and take log10(scaled_matrix + 1.01) to get a matrix with smallest number not equal to 0.

[zji90]

I encountered the same error even if I replaced 0 with a small number log10(1.01) or log10(1.1)