Trying to use MCIA for 16S and metabolomics, running into error

[rsmote]

Hello,

I'm trying to use MCIA for 16S and metabolomics data integration, but am getting an error.

The error reported is: ''svd' fail to convergence, 'eigen' used to perform singular value decompositionError in if (tab[i, i] < 0) { : missing value where TRUE/FALSE needed"

Here is the code I'm using: library(omicade4)

dataA<-read.csv("Final_metabolome.csv",header=T) dataB<-read.csv("Final_Relabund.csv",header=T) dataA<-dataA[,-1] dataB<-dataB[,-1] df.list<-list(dataA,dataB) BFT.mcia <- mcia(df.list,cia.nf=2,cia.scan=FALSE,nsc=T,svd=TRUE)"

This is where the error is reported. Any guidance would be appreciated. Thanks!

[mengchen18]

I am happy to look into this, but could you give me a small dataset that can reproduce the error. It's hard to guess from the error message itself.

Best,

[rsmote]

Thanks for the reply! I have attached two small example datasets. One is the metabolome and the other is 16S abundances for 100 rows each. I hope this helps.

Example_Relabund.txt Example_metabolome.txt

[mengchen18]

Hi, I don't see a problem, below is what I did. You can see if you can reproduce. If there's still an error, please paste the output of "sessionInfo()", you might have a different version.

library(omicade4) library(matrixStats)

make matrices

dataA<-read.delim("Example_metabolome.txt",header=T, stringsAsFactors = FALSE) dataB<-read.delim("Example_Relabund.txt",header=T, stringsAsFactors = FALSE) dA<-apply(dataA[-1, -1], 2, as.numeric) rownames(dA) <- make.names(dataA$Sample[-1], unique = TRUE) dB<-apply(dataB[-1, -1], 2, as.numeric) rownames(dB) <- make.names(dataB$Sample[-1], unique = TRUE)

remove constant rows

dA <- dA[rowVars(dA) > 0, ] dB <- dB[rowVars(dB) > 0, ] df.list<-list(d1=dA,d2=dB)

MCIA

BFT.mcia <- mcia(df.list, cia.nf=2,cia.scan=FALSE,nsc=T,svd=TRUE)

plot

plot(BFT.mcia)

sessionInfo

sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] matrixStats_0.52.2 omicade4_1.18.0 ade4_1.7-11 BiocInstaller_1.28.0

loaded via a namespace (and not attached): [1] MASS_7.3-47 compiler_3.4.1 tools_3.4.1 made4_1.52.0

[rsmote]

I was able to reproduce. Thanks so much for this! Sorry for the delay in response!