featurecounts_deseq2.r expects that sample names end in "_R1" etc and will trim the last 3 characters of the sample name to obtain the group ID for DESeq2. This will not work when there are 10 or more replicates per group. In this case, you end up with twice the expected number of experimental groups, because the underscore is retained in some replicates, for example: Tissue1 and Tissue1_. It would be safer to remove everything starting at the underscore.