error while running maaslin2 in R about maaslin2 HOT 7 CLOSED

Hi @negin1986 - sorry for the delay in getting back to you. Could you please send a minimum reproducible example so that I can debug?

from maaslin2.

Having similar error, curious if this was ever figured out?

from maaslin2.

I had the same Error in FUN(newX[, i], ...) : invalid 'type' (character) of argument error when I was trying to run Maaslin2 by supplying data frames as input instead of the string filepaths to the input files as in the demo (running in Rstudio).

I got a different error when I tried to read the demo files into data frames and run Maaslin2. To me, it seems ideal that the function would accept either data frames or filepaths as input.

from maaslin2.

Aynone had a solution for this? Did you manage to run it?

from maaslin2.

I have tried with your example files too and have the same output error:

2020-01-27 17:56:16 INFO::Running selected normalization method: TSS
Error in FUN(newX[, i], ...) : invalid 'type' (character) of argument
In addition: Warning message:
In vegan::decostand(features_norm, method = "total", MARGIN = 1, :
input data contains negative entries: result may be non-sense

Have no idea what's happening because I was using it until recently.

Thank you so much for the help.

Bahti

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I have had the same issue, even with the test data the package provides, but only when the input is a data frame from R; otherwise it works when providing the path to a file. I found a workaround by writing my tables to a tmp file and then executing the function, although it is kind of annoying having to do this

# Write files to tmp and execute
tmp_data = tempfile(pattern = "data")
write_delim(Relabund_data, tmp_data, delim = "\t")


tmp_metadata = tempfile(pattern = "metadata")
write_delim(Metadata_LMs, tmp_metadata, delim = "\t")

fit_data <- Maaslin2(tmp_data, tmp_metadata, "out/dir")

from maaslin2.

Dear Jacobo,
Thank you so much. Actually I managed to do as you suggested. I am so sorry that I forgot to add my working commands here. But I really appreciate your help too.
Cheers,
Bahti

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