Hi,

I'm using the function RUVg in the RUVSeq package to analyse my RNA-seq data and then to DEseq2. I have 50 samples. Im following the steps of Love et al. where as factor k they propose k=1 (https://bioconductor.org/packages/release/bioc/vignettes/RUVSeq/inst/doc/RUVSeq.html#filtering-and-exploratory-data-analysis) while in this site of Love et al. (https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#using-ruv-with-deseq2) they use k=2. The problem is i dont know whick k to use and what is doing exactly! My samples are changing a lot when k=2 (that are divided in 4 groups) especially in plotRLE. *i'm using the spike-ins as negative controls