**0**wrote:

I asked this question on SeqAnswers.

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):

A1 | A2 | B1 | B2 | |

Gene 1 | 0 | 0 | 692 | 1350 |

> dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition) > dds$condition <- factor(dds$condition, levels=c("A","B")) > dds <- DESeq(dds) > res<-results(dds,independentFiltering = F)

Results table:

baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |

Gene1 | 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