Dear DEseq developers,
        I have a few questions related to the normalization step in DEseq.
        It is stated that it will normalize the raw counts by library size,
but how the mathmatical idea is? would you mind giving a more detailed
explanation?
        Now I have two groups of metatranscriptome data, one group contain
H.pylori, the other not. For sure, I have some transcripts in the first
group that are from H.pylori but not is in group two.
        I am wondering if I want to do differential expression analysis for
these two groups, should I filter out the group specific transcripts before
putting into DEseq? Will this affect the normalization step?
Thanks!
best,
Laurie


-- 
Rui Luo
Lab phone : 310 794-7537
Geschwind Lab
Human Genetics Department
UCLA

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