Hi everybody, I'm currently working on a project which involves the measurement of genome-wide gene expression through deep-sequencing. We calculate the gene expression as RPKM as described in literature and then we apply a rank product analysis to get the differentially expressed genes. To apply the rank product statistic we use the Bioconductor RankProd package. Everything is fine except for one dataset (two replicates, for two conditions). When calling the topGene function and imposing a cutoff of 0.05, we have as a result an unfiltered list of genes. In particular in the list we find many genes with a pfp > 0.05. Unfortunately, I can not figure out what is wrong. Any ideas? The dataset can be find here
Thanks for your help.