I have a question related to ChIP-seq spike-in normalization as illustrated on the csaw vignette.
The idea of calculating a norm factor on the spikes data is great. But as mentionned in the vignette, using the normoffset function on the spike (...) assume that the library sizes are the same between spike.data and endog.data (...).
However, in my case, I did two seperate mappings (one on the foreign and one on the reference genome). It means that my lib.sizes are differents between the two genomes ...
So, is it still correct to use the norm factor calculated on the foreign genome (with its own lib.size), and to apply it to the counts from my reference genome ? using CPM function for instance ?
Apart of that I guess that with this mapping strategy, results can be very different with another normalization strategy such as DESeq for instance, as the lib.size is directly included into the scaling factor ... meaning that it will use the lib.size from my foreign genome ...
Many thanks for your comments.