SampleC-tNKT-liver-b Unknown None SampleC NONE 2 narrow SampleC-tNKT-liver-a Unknown None SampleC NONE 1 narrow SampleB-tNKT-liver-d Unknown None SampleB NONE 4 narrow
SampleB-tNKT-liver-c Unknown None SampleB NONE 3 narrow SampleB-tNKT-liver-b Unknown None SampleB NONE 2 narrow SampleB-tNKT-liver-a Unknown None SampleB NONE 1 narrow
SampleA-tNKT-liver-d Unknown None SampleA NONE 4 narrow SampleA-tNKT-liver-c Unknown None SampleA NONE 3 narrow SampleA-tNKT-liver-b Unknown None SampleA NONE 2 narrow SampleA-tNKT-liver-a Unknown None SampleA NONE 1 narrow Hi Rory, It took me some time to get back on this, but here are the things you asked for:ĭata <- DiffBind::dba(sampleSheet = samples, peakFormat="narrow", scoreCol = 5, filter = 20, config=ame(RunParallel=TRUE) ) Loaded via a namespace (and not attached): DiffBind_2.6.1 SummarizedExperiment_1.8.0 parallel stats4 stats graphics grDevices utils datasets LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 The following objects are masked from âpackage:matrixStatsâ:ĬolMaxs, colMins, colRanges, rowMaxs, rowMins, rowRangesīLAS: /usr/lib/openblas-base/libblas.so.3 The following objects are masked from âpackage:Biobaseâ: 'citation("Biobase")', and for packages 'citation("pkgname")'. Vignettes contain introductory material view with Loading required package: SummarizedExperiment The following object is masked from âpackage:baseâ: Table, tapply, union, unique, unsplit, which, which.max, which.min Rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, Mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, Grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, The following objects are masked from âpackage:baseâ:ĪnyDuplicated, append, as.ame, cbind, colMeans, colnames,ĬolSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, The following objects are masked from âpackage:statsâ: ParLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from âpackage:parallelâ:ĬlusterApply, clusterApplyLB, clusterCall, clusterEvalQ,ĬlusterExport, clusterMap, parApply, parCapply, parLapply, How could I fix it?Įrror in heights * sapply(called, function(x) x) : non-conformable arrays Then I run dba.count using summits=150 with score default. when loading Diffbind 2.6, there is no warnings.Ģ. I still failed run with dba.count, however.
Error in taply update#
In both cases, the error is fixed but only the second one will fix it for every averaging formula you might use.Hello, Rory, Thank you for suggestions at C: Warnings when update DiffBind and running errors. It involves making sure that the argument is formatted properly by adding “FUN =” in front of the averaging formula. This approach to fixing the problem works regardless of the averaging formula you are using. It is a simple solution if you are looking for the mean value of the vector argument. This is the simplest fix of this error because it uses the default averaging formula. The second approach involves producing the correct form of the averaging formula. This only works if you are calculating mean value, because that is the default. The first involves removing the average averaging formula. There are two ways of correcting this error. This clearly traces down the source of the error message to the averaging formula. In this example, the averaging function is simply unused and there is no error message. In this case, it is being set to “mean” and thereby producing the mean value of the x vector. In this example, we have the ave() function setting the averaging function properly.
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