Hi,

I want to combine DESeq2 and CQN to normalize the count matrix of ATAC_seq data.

I follow this step:

cqnOffset <- cqn.subset$glm.offset   
cqnNormFactors <- exp(cqnOffset)
normalizationFactors(object_cqn) <- cqnNormFactors
object_cqn <- DESeq(object_cqn,parallel=T)

But DESeq2 mannul describes that normalization factors, if present, will always be used in the place of
size factors.

According to the above step, sizeFactors will not be considered. How can I solve this problem?

Thanks.

See the man page for ?cqn under the description of the output glm.offset

(cqn corrects for size factors and the glm.offset contains size factor correction)