Hi All,

I have been using DESeq2 to perform differential gene expression analysis between two groups but I do not have house keeping genes in the data set. Is it still possible to do DESeq calculations without the house keeping genes? and I do not have all the genes expressed across all subjects/samples. 

I have the following error message calculating size factors:

> dds <- DESeq(dds)

>estimating size factors

>Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  : 

>every gene contains at least one zero, cannot compute log geometric means

Any help would be appreciated. 

Thank you.

Gajender
DESeq2 by default doesn't use housekeeping genes. It makes the assumption that most genes are not diferentially expressed, and corrects based on the gene with the median expression

But your problem is exactly as it says; the default normalization method calculates the geometric mean of each gene, that is not possible when a gene has a sample with zero counts.  Some genes with some zeroes are fine, the normalization function just ignores them, but in your data, every single gene is being excluded for that reason.  The default method of normalization will not work with your dataset as is.  If you have a few samples with very few reads, omitting them might fix the problem.