[BioC] DESeq2 Error in estimateSizeFactorsForMatrix

[Simon Anders]

Dear Caleb

On 30/05/14 16:59, Caleb Bostwick [guest] wrote:
 > Could you please help me or direct me to a source where I might find 
 > a solution to my error problem? A "Google search" on the error did
 > not return useful results. Thank you very much.

For starters, check whether the claim of the error message is actualy true:
> Error in estimateSizeFactorsForMatrix(counts(object), locfunc, geoMeans = geoMeans) :
>    every gene contains at least one zero, cannot compute log geometric means

Does every gene contain a zero in at least one of the samples? If so, 
how comes?

   Simon