[BioC] DiffBind - error when setting manual contrast groups

Giuseppe Gallone giuseppe.gallone at dpag.ox.ac.uk
Thu Nov 7 17:03:07 CET 2013


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



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