Hi there, 

When I am running the DESeq pipeline on the dds object and getting this error message.

    > dds_res<-DESeq(dds_PvsN)
    estimating size factors
    Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  : 
      every gene contains at least one zero, cannot compute log geometric means
    In addition: Warning message:
    In class(object) <- "environment" :
      Setting class(x) to "environment" sets attribute to NULL; result will no longer be an S4 object

What strategy should be applied to resolve this conflict?

Thank you very much!

Imran 


I encountered this error only once in the past. It is as stated: every gene in your data has at least one zero value, and this creates an issue for the size-factor calculation.

Solutions:

 1. add a pseudo-count value of '1' to your data
 2. use: `estimateSizeFactors(dds_PvsN, type = 'iterate')`

Kevin
