Hi I'm testing DiffBind using a contrast between two groups containing only one sample each. According to the manual, this is highly discouraged, but possible in principle. I manually set the contrast groups using the construct tamoxifen = dba.contrast(tamoxifen, tamoxifen$masks$Responsive, tamoxifen$masks$Resistant, "Responsive", "Resistant") I then run dba.analyze as usual tamoxifen = dba.analyze( tamoxifen, method=DBA_ALL_METHODS, bFullLibrarySize=TRUE, bTagwise=TRUE, bParallel=TRUE ) For dba.score, counts are obtained using DBA_SCORE_TMM_READS_EFFECTIVE. When I run dba.analyze I get the following Error in d$span : $ operator is invalid for atomic vectors Best regards Giuseppe