Error message during running runSCENIC_3_scoreCells()

[wulc21]

Hi Dear Professor, When I running the SCENIC workflow according to the tutorial file from http://127.0.0.1:12249/library/SCENIC/doc/SCENIC_Running.html, I encounter the following Error Massage when I running "scenicOptions <- runSCENIC_3_scoreCells(scenicOptions, exprMat_log)“code ， I have followed the vignette of runSCENIC_3_scoreCells from http://127.0.0.1:12249/library/SCENIC/doc/detailedStep_3_scoreCells.html#create-rankings, and find the error massage "Catched error in AUCell_buildRankings() or in the histogram plot: 没有".openDev"这个函数" when I running the Create rankings** step. Please help me solve the problem. Thank you very much.

################Error massage I encountered during I running the SCENIC workflow#############

scenicOptions <- runSCENIC_1_coexNetwork2modules(scenicOptions) 14:54 Creating TF modules Number of links between TFs and targets (weight>=0.001): 6139 [,1] nTFs 8 nTargets 770 nGeneSets 47 nLinks 17299 scenicOptions <- runSCENIC_2_createRegulons(scenicOptions, coexMethod=c("top5perTarget")) # Toy run settings 14:54 Step 2. Identifying regulons tfModulesSummary: [,1] top5perTarget 8 14:54 RcisTarget: Calculating AUC Scoring database: [Source file: mm9-tss-centered-10kb-7species.mc9nr.feather] 14:54 RcisTarget: Adding motif annotation Number of motifs in the initial enrichment: 867 Number of motifs annotated to the matching TF: 126 14:54 RcisTarget: Prunning targets 2021-01-13 14:54:22.875 R[17516:902799] IMKClient Stall detected, please Report your user scenario attaching a spindump (or sysdiagnose) that captures the problem - (imkxpc_bundleIdentifierWithReply:) block performed very slowly (1.29 secs). 14:55 Number of motifs that support the regulons: 126 [1] "Saving a widget with selfcontained = TRUE requires pandoc. For details see:\nhttps://github.com/rstudio/rmarkdown/blob/master/PANDOC.md" Warning message: package ‘AUCell’ was built under R version 4.0.3 > scenicOptions <- runSCENIC_3_scoreCells(scenicOptions, exprMat_log) 14:55 Step 3. Analyzing the network activity in each individual cell Number of regulons to evaluate on cells: 14 Biggest (non-extended) regulons: Tef (405g) Sox9 (150g) Irf1 (104g) Sox8 (97g) Sox10 (88g) Dlx5 (35g) Stat6 (27g) Quantiles for the number of genes detected by cell: (Non-detected genes are shuffled at the end of the ranking. Keep it in mind when choosing the threshold for calculating the AUC). min 1% 5% 10% 50% 100% 46.00 58.99 77.00 84.80 154.00 342.00

Catched error in AUCell_buildRankings() or in the histogram plot: assignment of an object of class “SimpleAssays” is not valid for slot ‘assays’ in an object of class “aucellResults”; is(value, "Assays_OR_NULL") is not TRUE Error in saveRDS(aucellRankings, file = getIntName(scenicOptions, "aucell_rankings")) : 找不到对象'aucellRankings'

#################Error diagnosis during I trying the runSCENIC_3_scoreCells() command line by line ######### tryCatch({ .openDev(fileName=getIntName(scenicOptions, "aucell_genesStatsPlot"), devType=getSettings(scenicOptions, "devType")) aucellRankings <- AUCell_buildRankings(exprMat, nCores=nCores, plotStats=TRUE, verbose=getSettings(scenicOptions, "verbose")) abline(v=aucellRankings@nGenesDetected["1%"], col="skyblue3", lwd=5, lty=3) dev.off() },error = function(e) { message("Catched error in AUCell_buildRankings() or in the histogram plot: ", e$message) })

[cyybhfq]

请问您解决这个问题了嘛？我也遇到了同样问题

[wulc21]

解决了，比较久了。好像是因为依赖的包版本不兼容的问题，麻烦你看一下我后面的回复。我记得好像回复过。

发自我的iPhone

在 2021年12月15日，下午10:42，cyybhfq @.***> 写道：

 请问您解决这个问题了嘛？我也遇到了同样问题

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