I try to use DEseq2 to Identify the changed genes in my two chip-seq data.
Because our experiment design is use the spike-in chromatin to do
normalization, so we do not need estimate the effective library size.
I just assign a value to sizeFactors like:
> sizeFactors(data) <-- c(-1,-2) > sizeFactors(data) > hj67 hj68 1 2 > res = nbinomTest(data, "wt", "ko" );
> My question is :
1) I am not sure whether i can do like this ?
2) Another question is: when I want to the sizeFactors is 1 and 2, why I need input -1 and -2 ?