plotProfile Errors of DiffBind

Question

[lijiangres]

I am using the published data (doi.org/10.1111/nph.19791) , working on comparing the differential binding sites of H3K27me3 between the endo WT and crwn samples, three biological replicates for each condition. H3 signal as control in my analysis.

Thus far, the computational steps have proceeded smoothly (excluding the use of blacklist and greylist). However, I have encountered a problem at the final stage of generating the profile plot. Despite attempting to disable parallel processing and thoroughly checking the consistency of my data, I have been unable to resolve the issue.

profiles <- dba.plotProfile(dbObj5)
Generating report-based DBA object...
Generating profiles...
**Error in value[[3L]](cond): 
  profileplyr error: Error: BiocParallel errors
  1 remote errors, element index: 1
  5 unevaluated and other errors
  first remote error:
Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in DataFrame(..., check.names = FALSE): different row counts implied by arguments**

Here is the dataframe

data completement check
I> nrow(dbObj5$binding)
[1] 4568
> complete_cases <- complete.cases(dbObj5$binding)
sum(complete_cases)
sum(!complete_cases)
[1] 4568
[1] 0


sessionInfo()
R version 4.4.1 Patched (2024-09-28 r87201 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese
(Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
time zone: Etc/GMT-8
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] profileplyr_1.22.0 DiffBind_3.16.0
SummarizedExperiment_1.36.0
[4] Biobase_2.66.0 MatrixGenerics_1.18.1 matrixStats_1.5.0
[7] GenomicRanges_1.58.0 GenomeInfoDb_1.42.3 IRanges_2.40.1
[10] S4Vectors_0.44.0 BiocGenerics_0.52.0 BiocParallel_1.40.0

[lijiangres]

R code

>library(BiocParallel)

>register(SerialParam(), default=TRUE)  
>options(DelayedArray.auto.parallel=FALSE) 
> library(DiffBind)

> library(profileplyr)

> dbObj <- dba(sampleSheet="samplesheet.csv")
# count
> dbObj2 <- dba.count(dbObj, summits = TRUE)
# normalize
> dbObj3 <- dba.normalize(dbObj2) 
# set contrast
> dbObj4 <- dba.contrast(dbObj3,reorderMeta=list(Condition="wild"))
# analysis
> dbObj5 <- dba.analyze(dbObj4) # default threshold of FDR <= 0.05,method of DESeq2
# profile
> dba.plotProfile(dbObj5)

Generating report-based DBA object...
Generating profiles...
Error in value[[3L]](cond): 
  profileplyr error: Error: BiocParallel errors
  1 remote errors, element index: 1
  5 unevaluated and other errors
  first remote error:
Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in DataFrame(..., check.names = FALSE): different row counts implied by arguments

[this_is_me_trying]

Hello, I'm having the same problem. Did you find a solution?

Answer 1

[lijiangres]

No, I gave up for the published data. It looks like there's missing data somewhere. While the program works for my own data.