Random effect model RNAseq

Question

[a.stef.44]

Hi everyone,

I would like to perform random effect model (RMA) using LFC from DESeq2 and Var. I have four different studies and I planned to use REML (Restricted maximum likelihood) estimator, I have one dataset composed of LFC values of Study1, Study2, Study3 and Study4 (in columns) and different data frame composed of Var for Study1, Study2, Study3 and Study4 (in columns). The function I found is form metafor package https://cran.r-project.org/web/packages/metafor/vignettes/metafor.pdf:

m_re <- rma(yi = df$d,     
            vi = df$vi)  

But in my case I don't know how to organize data frame to be able to perform RMA, as now following function I can only do something like this, but it does not make any sense.

rem<-rma(yi=combined.lfc$Study1,
        vi=combined.var$Study1)

Thank you in advance for your help!