We have RNA-seq data for 6 individuals showing one phenotype and 6 showing another (12 total samples). Before doing a diff. analyses between two groups of 6 each, we'd like to assess the variability within each group using the FPKM values given by cufflinks. Can someone point out a good method? Do EdgeR / DESeq etc. do this? All suggestions welcome.
I think in the microarray world there are several tests available for this, and I am just wondering if there is anything analogous for RNA-seq counts data.
Thanks, forum.
what are the standard within-sample metrics for microarrays?