Deseq Sizefactors Help
I try to do the diff analysis by DESeq on two samples coming from two different condition without replicate
I run the script of DESeq and when I give the library size of my sample, the size factor is 1 for both conditions
libsizes <- c( Cond1 =80040653, Cond2 =360265740)
I don't understand this estimation?
when I don't give the libsizes, it become
Could you please explain for me this issue?
Thanks in advance
The author of DESeq wrote a post on SeqAnswers a while back about how the size factors thing work in DESeq. I'll try to find the post, but basically it normalizes the datasets by:
-Take the geometric mean of each condition for a gene and use that as the reference expression data set.
-For each condition, get a list of quotients of each gene expression value to its reference expression.
-The median of each condition quotient list is the normalization factor for that data set.
Here is the post:
I don't see where in the documentation it says libsizes is a magic word.
Either use the estimateSizeFactors to use your count data as the source of the estimate, or set it manually using sizeFactors.
Now, why are there so many Sara's?
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