Hi, I have a CUT&RUN experiment with 3 groups, 2 replicates. I ran the following:
affinity binding matrix
DBA1_3 <- dba.count(DBA1_3, bUseSummarizeOverlaps = TRUE)
normalize
DBA1_3 <- dba.normalize(DBA1_3)
Establishing contrast groups
DBA1_3 <- dba.contrast(DBA1_3, group1 = DBA1_3$masks$M, group2 = DBA1_3$masks$C, name1 = "M", name2 = "C")
DBA1_3 <- dba.contrast(DBA1_3, group1 = DBA1_3$masks$P, group2 = DBA1_3$masks$M, name1 = "P", name2 = "M")
DBA1_3 <- dba.contrast(DBA1_3, group1 = DBA1_3$masks$P, group2 = DBA1_3$masks$C, name1 = "P", name2 = "C")
DBA1_3 <- dba.analyze(DBA1_3, method=DBA_EDGER, bGreylist = FALSE)
This worked nicely when I used dba.show. However, when I tried to write dba.report for the different contrasts using:
Dreport1<- dba.report(DBA1_3, method=DBA_EDGER, contrast=1)
Dreport2 <- dba.report(DBA1_3, method=DBA_EDGER, contrast=2)
Dreport3 <- dba.report(DBA1_3, method=DBA_EDGER, contrast=3)
The first report runs okay. The other two give me the following error:
Error in .new_IRanges_from_start_width(start, width) : 'start' or 'width' cannot contain NAs
sessionInfo() gives me DiffBind version 3.4.6. Why would the first report run ok but not the other two??
Thank you for your quick response. I started using the old group1/group2 I think because I started with unequal groups (n=3 for 2 groups, n=2 for one) and it kept only returning the contrast comparing the 2 groups with n=3. Since I am new here, what is the best way to give you access to the DBA object?
You can email me at the maintainer's email address listed on the
DiffBind
page on theBioconductor
site. If you can save your DBA objectDBA1_3
usingdba.save()
, store it someplace I can access it (like Dropbox), and send me the link, I can have a look.You should be able to set the contrasts you want using a design formula. Here's an example using the sample data: