Hello, I am using DESeq2 for a DGE analysis and I have been stocked on this specific error.

dds <- DESeqDataSetFromMatrix(countData = all.data.set_v3,
                       colData = all.group_v3,
                       design = ~ group)

#converting counts to integer mode
#Warning: some variables in design formula are characters, converting to factors

dds@assays@data@listData[["counts"]] <- as.matrix(dds@assays@data@listData[["counts"]]+1)
#run that in order to avoid the following error (i know it is not the best solution but i am passing a cap:
#estimating size factors
#Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  : 
#  every gene contains at least one zero, cannot compute log geometric means

dds@assays@data@listData[["counts"]] <- as.integer(dds@assays@data@listData[["counts"]] )
#run this in order to avoid the following error:
#estimating size factors
#Error in validObject(object) : 
# invalid class “DESeqDataSet” object: the count data is not in integer mode

dds1 <- DESeq(dds) #gives me the following
#estimating size factors
#Error in h(simpleError(msg, call)) : 
#  error in evaluating the argument 'x' in selecting a method for function 'rowMeans': 'dimnames' applied to non-array