Is it possible to skip the estimateSizeFactor step in Deseq2 and define your own size factors? If I just replace the size factor vector with my own values, will the down-stream DE steps use these values? I am pretty new with R so it would be very helpful if I can see some example code on how to do this. 
Yes you can, that is what I can read from the below link

Take a look [here][1] and [here][2]

There was a [post][3] from where Damian you already replied few years back where I can see Jeremy replied that you can set the size factor manually as well with `sizeFactors`

*dds <- estimatesizefactors(dds)<="" code=""> See DESeq for a description of the use of size factors in the GLM. One should call this function after DESeqDataSet unless size factors are manually specified with sizeFactors. Alternatively, gene-specific normalization factors for each sample can be provided using normalizationFactors which will always preempt sizeFactors in calculations. Internally, the function calls estimateSizeFactorsForMatrix, which provides more details on the calculation.*


  [1]: http://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/estimateSizeFactors
  [2]: http://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/sizeFactors
  [3]: https://www.biostars.org/p/12273/