diffbind dba.report error
Entering edit mode
4 months ago
jellybean5 • 0

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)


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??

diffbind R • 316 views
Entering edit mode
4 months ago
Rory Stark ★ 1.5k

If I can get access to your DBA object DBA1_3, I can have a look.

Is there a particular reason you are using the old-style group1/group2 contrasts instead of the preferable method of using a design formula and specifying the conditions to test using the contrast parameter?

Entering edit mode

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?

Entering edit mode

You can email me at the maintainer's email address listed on the DiffBind page on the Bioconductor site. If you can save your DBA object DBA1_3 using dba.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:


tamoxifen <- dba.contrast(tamoxifen, 
tamoxifen <- dba.contrast(tamoxifen, 
                          contrast=c("Tissue","ZR75", "MCF7"))
tamoxifen <- dba.contrast(tamoxifen, 
                          contrast=c("Tissue","T47D", "MCF7"))

tamoxifen <- dba.analyze(tamoxifen)

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