I have a short question about TMM normalization in csaw.
I would like to normalize ChIP-seq histone marks data, and compare samples (WT vs KO).
Before starting, I have my bam files, and results from peak calling. Here is my plan ;
1- Run bin counts over large genomic bins (10kb), where peaks locations were removed. So basically, the idea is to count over the background only (using windowCounts)
2- Counts the reads on peak regions (using regionCounts)
3- Normalize the peak counts using the scaling factors calculated on background only
counts.peaks <- normOffsets(counts.bg, se.out=counts.peaks)
However, here, I have an issue with the library size.
Error in .local(object, ...) :
library sizes of 'se.out' and 'object' are not identical
The message is clear, but how can I fix it ?
Any feedback is welcome.