sva for RNA-Seq data without known phenotype
You can just remove the first component from the dataset by setting the first eigenvalue to 0 in the diagonal matrix and then multiplying the SVD matrices. 

I am not sure which R code you are using to estimate the components (I have a comparison of PCA code in R on https://github.com/aedin/ODSC_2018/tree/master/PCA_vignette)  

In ade4 R package, there is a function reconst() which reconstructs data from a selection of components: https://rdrr.io/rforge/ade4/man/reconst.html

Happy to provide code to do this in other PCA versions if needed
Aedin Culhane