I have a RNASeq paired-end data from two batches (8 samples from batch1, and 7 samples from batch2). After alignment using TopHat2, then I got count using HTseq-count, and FPKM value via Cufflinks. A big batch effect can be viewed in PCA using both log10(raw count) and log10(FPKM) value.
I can NOT use the block factor in edgeR to remove batch effect since I need to first obtain residuals after adjusting for batch effect, then test the residuals for hundreds of thousands of SNPs (eQTL analysis).
My question is how to remove batch effect without using edgeR:
1. is SVA ok for such a small sample size (N=15)?
2. If SVA does not work, any other suggestions?