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When I used dba.cout with DiffBind， the following error occurred.
dbObj <- dba(sampleSheet="SampleSheet.csv") FAD1 AD 1 narrow FAD2 AD 2 narrow WT1 WT 1 narrow WT2 WT 2 narrow dbObj <- dba.count(dbObj, bUseSummarizeOverlaps=TRUE) Computing summits... Re-centering peaks... Error in if (sum(tokeep) < length(tokeep)) { : missing value where TRUE/FALSE needed
I have tried in Rstudio server or R in linux, both failed. I have attached the dir of files and the SampleSheet.csv
Here is the head of bed file
Can anyone help?
Can you confirm the version you are using (
sessionInfo())?
Also, if you can try setting
filter=0in the call to
dba.count(), it would be informative to know if that worked.
R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS
Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8
loaded via a namespace (and not attached): [1] compiler_4.1.1 fastmap_1.1.0 htmltools_0.5.2 tools_4.1.1 yaml_2.2.1 rmarkdown_2.11 [7] knitr_1.37 xfun_0.29 digest_0.6.29 rlang_0.4.12 evaluate_0.14
I still don't see the
DiffBindversion in this posting? What does
package.version("DiffBind")return?
If you don't mind, I'll continue the response to this at the duplicated entry on the Bioconductor support forum: 
Check there for more information.