Dear Bioconductor Team,
We sequenced samples A with 4 replicates and B with 4 replicates last year, and C with 3 replicates this year. Since there are no overlapped samples, I can't include batch effect in the DESeq model. So I tried to run SVAseq, and got 9 SVs.
However, the online workflow https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html, does not calculate the number of SVs, only used 2.
My question is: should I go with 2 or 9 for the subsequent DESeq2 analysis here?
Thanks for any inputs!