SEQanswers (
-   RNA Sequencing (
-   -   DESeq2 and zero counts in one condition (

gmatt 01-09-2015 08:37 AM

DESeq2 and zero counts in one condition
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
0 0 692 1350

Results table:

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?


Michael Love 01-09-2015 11:32 AM

question answered on

All times are GMT -8. The time now is 07:52 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.