I have five different cell type  i m doing both rld and vsd transformation .I want the vsd data to perform other analyiss such as Self organising maps as well as WGCNA . How can i take out the vsd transformed data 

Im using this code 

    vsd <- varianceStabilizingTransformation(dds, blind=FALSE)

To get all my normalised data set im using this code 

    resOrdered <- res[order(res$padj),]
    summary(resOrdered)
    resdata <- merge(as.data.frame(res), as.data.frame(counts(dds, normalized=TRUE)), by="row.names", sort=FALSE)
    names(resdata)[1] <- "Gene"
    
    head(resdata)
    dim(resdata)
    ## Write results
    write.csv(resdata, file="Primary_cell_line__normalised_data.csv",row.names = FALSE,quote = F)

But this is for the rlog transformation what i saw in the manual if im not wrong , how can i do the same for vsd transformed data ?Any suggestion or help would be highly appreciated  




Your second chunk of code is not for rlog transformed data but for the normalised counts. If you want the data in the same shape as the normalised counts but for rlog or vst transformed data then you need something along the lines of:

    vsd <- assay(varianceStabilizingTransformation(dds, blind=FALSE))
    rlog <- assay(rlogTransformation(dds, blind=FALSE))