I am trying to perform
dba.analyze in DiffBind, but I am unclear on the use of Blacklists/Greylists to obtain differentially bound sites. From my reading of the manual, I thought greylists needed to be set to
TRUE to be invoked, though it appears I am attempting to compute a blacklist/greylist (see below)- is this a default setting for
In any case, while I plan to consider applying a greylist in another analysis, how can I apply the simplest
dba.analyze in order to retrieve DESeq sites? Note that I have provided input controls in my sample sheet.
> Bcontrast 6 Samples, 1173 sites in matrix: ID Condition Treatment Replicate Reads FRiP 1 wt1b WT none 1 16902874 0.20 2 mt1b MT none 1 14594474 0.13 3 wt2b WT none 2 16878697 0.22 4 mt2b MT none 2 14289354 0.15 5 wt3b WT none 3 18699283 0.24 6 mt3b MT none 3 15424246 0.20 Design: [~Condition] | 1 Contrast: Factor Group Samples Group2 Samples2 1 Condition MT 3 WT 3 > Bdiff <- dba.analyze(Bcontrast) Applying Blacklist/Greylists... Genome detected: Scerevisiae.UCSC.sacCer3 Applying blacklist... No blacklist found for BSgenome.Scerevisiae.UCSC.sacCer3 Counting control reads for greylist... Building greylist: C:/Ben/ChIPseq_analyses/bb.202202.ChIPseq/aws/bams/A1.bam Blacklist error: Error in sample.int(length(x), size, replace, prob): cannot take a sample larger than the population when 'replace = FALSE' Unable to apply Blacklist/Greylist. > dba.show(Bdiff, bContrasts=TRUE) Factor Group Samples Group2 Samples2 1 Condition MT 3 WT 3