is there any requirements to the expression matrix?

[Yunuuuu]

I'm very interested in finding such package for constrcuting ceRNA network.
I have read the paper for SPONGE theory where conduct construction of a pan-cancer ceRNA network with the data from UCSC, and expression matrix is performed a log2 transformation, as I known, the unit of the data in UCSC is log2(count+1), so I don't know whether there is some requirements to the expression matrix? Can I use normalized counts which is transformed via count(matrix, normalized = T)? or Can I use vst function from DESeq2 package to transform expression matrix?

[mlist]

We do not have requirements for the expression matrix. SPONGE operates on (partial) correlations and as such is, in theory, relatively robust to normalization and transformation of the expression data. I recommend you compare gene-gene as well as gene-miRNA correlations before and after the operation to see if it had any (unwanted) effect.

[Yunuuuu]

Thanks for your help

We do not have requirements for the expression matrix. SPONGE operates on (partial) correlations and as such is, in theory, relatively robust to normalization and transformation of the expression data. I recommend you compare gene-gene as well as gene-miRNA correlations before and after the operation to see if it had any (unwanted) effect.