Missing genes and normalisation of RSEM output using EBSeq
Yes, that blog post does represent just one guy's opinion (hi!) and it does date all the way back to 2014, which is, like, decades in genomics years. :-) By the way, there is quite a bit of literature discussing the improvements that expected read counts derived from an Expectation Maximization algorithm provide over raw read counts. I'd suggest reading the RSEM papers for a start[1][2].

But your main question is about the mechanics of running RSEM and EBSeq. First, RSEM was written explicitly to be compatible with EBSeq, so I'd be very surprised if it does not work correctly out-of-the-box. Second, EBSeq's MedianNorm function worked very well in my experience for normalizing the library counts. Along those lines, the blog you mentioned above has another post that you may find useful.

But all joking aside, these tools are indeed dated. Alignment-free RNA-Seq tools provide orders-of-magnitude improvements in runtime over the older alignment-based alternatives, with comparable accuracy. Sailfish was the first in a growing list of tools that now includes Salmon and Kallisto. When starting a new analysis from scratch (i.e. if you ever get the original FASTQ files), there's really no good reason not to estimate expression using these much faster tools, followed by a differential expression analysis with DESeq2, edgeR, or sleuth.



1Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN (2010) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics, 26(4):493–500, doi:10.1093/bioinformatics/btp692.

2Li B, Dewey C (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12:323, doi:10.1186/1471-2105-12-323.