[BioC] re incomplete analysis in Deseq

Simon Anders anders at embl.de
Tue Mar 6 23:38:19 CET 2012


On 2012-03-06 22:21, Steve Lianoglou wrote:
> Couldn't we just-as-well adapt the estimateSizesFactorsForMatrix
> function to step over the (row,col) bins that have the 0 counts
> instead of skipping over rows that only have 1 0 element?

This might cause a bit of a bias, as we censor data which might pull 
down data. As a compromise, I am tempted to suggest adding a 
pseudocount, e.g., to add something like 0.1 to all values to avoid the 
zeroes. This also causes some bias but a less severe one. Of course, I 
now pulled the value 0.1 out of thin air, and cannot quite come up with 
a good justification for it.


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