DESeq2 and zero counts in one condition

[gmatt]

Does anyone know how DESeq2 handles genes that have zero counts in one condition and >0 counts in another?

My results output shows that these genes have a positive log2 fold-change value, but I do not understand how DESeq2 arrives at this number if it is taking the log of a ratio, in which the numerator is divided by zero.

Count data (letters are conditions; numbers are replicates):

Gene1:
A1 A2 B1 B2
0 0 692 1350

Results table:

Gene1:
baseMean log2FoldChange lfcSE stat pvalue padj
585.1394 11.78521 1.458913 8.078076 6.579644e-16 3.884571e-15


I know that DESeq1 gave an 'Inf' value in these cases, but how does DESeq2 arrive at a real number value?

Thanks

[Michael Love]

question answered on support.bioconductor.org