Hi, I was wondering if anyone can provide some suggestion as to what statistical tests I can use for differential gene expression with RPKM values.
I am stuck with RPKM as DESeq or edgeR is not an option for me unfortunately. I have generated some RNA-Seq data from a dozen tissue samples collected from patients with 2 disease phenotypes (n=6 for each group) and I would like to compare my result to the published RNA-Seq data using in vitro systems. Unfortunately the authors of the published paper only provided a table on RPKM values (and singleton as well for each of the tested conditions!). They also did not deposit any of the fastq files into any database so I cannot even re-do the alignment.
In this scenario where I have no raw counts on the published data and uneven group size, is there anyway that I can still reliably compare my data to the existing ones and do differential expression analysis? Any suggestion will be very helpful!