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zdk123 / SpiecEasi

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
GNU General Public License v3.0
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cross-domain interactions #255

Open gastronaut82 opened 8 months ago

gastronaut82 commented 8 months ago

Hi there,

I'm trying to run a cross-domain analysis using ITS2 data (2 fungal taxa) and 16s data, using: spiec_result_gr1 <- multi.spiec.easi(list(counts_hmp216S, counts_hmp2prot), method='mb', nlambda=40, lambda.min.ratio=1e-2, pulsar.params = list(thresh = 0.05))

However, I keep getting the following error. I've tried filtering in multiple ways, but the same thing keeps happening. How to fix this? Secondly, is this supposed to be performed only on count data, or on compositional i.e. relative abundance data?

ERROR message:

Applying data transformations... Error in if (max < min) stop("Did you flip min and max?") : missing value where TRUE/FALSE needed In addition: Warning message: In spiec.easi.list(datalist, method = method, sel.criterion = sel.criterion, : input list contains data of mixed classes.

gastronaut82 commented 8 months ago

Nevermind - I figured this problem out - it was because of columns that contained zeroes.