Hello,
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 dba.analyze
?
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.
Thanks,
> 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
Thank you!