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License: MIT License
Interactive Differential Expression Analyzer
License: MIT License
when i try to start IDEA it gives the following error
ERROR: could not find function "bsProgressBar"
was working fine till last week, Is there any dependency im missing?
Warning: Error in tag: could not find function "bsProgressBar"
Stack trace (innermost first):
60: tag
59: tags$div
58: div
57: tag
56: tags$div
55: div
54: tag
53: tags$div
52: div
51: tag
50: tags$div
49: div
48: tag
47: tags$div
46: div
45: tagList
44: attachDependencies
43: bootstrapPage
42: shinyUI
2: shiny::runApp
1: runIDEA
Error : could not find function "bsProgressBar"
Thank you
hi,
When I try to run idea, it starts but when I upload a file or use example data, it stuck in loading in progress screen and don't proceed further, the following is the message displayed in the terminal.
library(IDEA)
runIDEA()
Loading required package: shiny
Listening on http://127.0.0.1:3759
Loading required package: RJSONIO
Loading required package: plyr
Attaching package: ‘shinysky’
The following object is masked from ‘package:shiny’:
actionButton
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:plyr’:
rename
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:plyr’:
desc
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Warning in is.na(x[[i]]) :
is.na() applied to non-(list or vector) of type 'environment'
'BiocParallel' did not register default BiocParallelParams:
invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘.uid’, ‘RNGseed’ must be length 1
invalid class “MulticoreParam” object: 2: ‘.clusterargs’, ‘.controlled’, ‘logdir’, ‘resultdir’ must be length 1
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:DESeq2’:
plotMA
The following object is masked from ‘package:BiocGenerics’:
plotMA
Attaching package: ‘gplots’
The following object is masked from ‘package:IRanges’:
space
The following object is masked from ‘package:S4Vectors’:
space
The following object is masked from ‘package:stats’:
lowess
Loading required package: combinat
Attaching package: ‘combinat’
The following object is masked from ‘package:utils’:
combn
Loading required package: splines
Loading required package: impute
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following object is masked from ‘package:SummarizedExperiment’:
rowRanges
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
The following object is masked from ‘package:plyr’:
count
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Attaching package: ‘NOISeq’
The following object is masked from ‘package:edgeR’:
rpkm
Loading required package: grid
Loading required package: futile.logger
Attaching package: ‘RobustRankAggreg’
The following object is masked from ‘package:Matrix’:
rankMatrix
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
[1] "condition"
Warning: Error in checkContrast: 'contrast', as a character vector of length 3, should have the form:
contrast = c('factorName','numeratorLevel','denominatorLevel'),
see the manual page of ?results for more information
Stack trace (innermost first):
97: checkContrast
96: results
95: DEseqGetNBDEdata [/usr/local/lib/R/site-library/IDEA/IDEA/server.R#1061]
94: reactive:getDEseqResultTable [/usr/local/lib/R/site-library/IDEA/IDEA/server.R#1024]
83: getDEseqResultTable
82: renderDataTable [/usr/local/lib/R/site-library/IDEA/IDEA/server.R#1032]
81: func
80: origRenderFunc
79: output$DEseqTable
2: shiny::runApp
1: runIDEA
*** caught segfault ***
address 0xb7, cause 'memory not mapped'
Traceback:
1: .External("cairo_create_new_device", as.character(ctype), file, width, height, pointsize, bg, canvas, umpl, dpi, ..., PACKAGE = "Cairo")
2: Cairo(width, height, type = "png", file = filename, pointsize = pointsize, bg = bg, res = res, ...)
3: pngfun(filename = filename, width = width, height = height, res = res, ...)
4: (function (func, filename = tempfile(fileext = ".png"), width = 400, height = 400, res = 72, ...) { if (capabilities("aqua")) { pngfun <- grDevices::png } else if ((getOption("shiny.usecairo") %OR% TRUE) && nchar(system.file(package = "Cairo"))) { pngfun <- Cairo::CairoPNG } else { pngfun <- grDevices::png } pngfun(filename = filename, width = width, height = height, res = res, ...) op <- graphics::par(mar = rep(0, 4)) tryCatch(graphics::plot.new(), finally = graphics::par(op)) dv <- grDevices::dev.cur() on.exit(grDevices::dev.off(dv), add = TRUE) func() filename})(function () { success <- FALSE tryCatch({ grDevices::dev.control(displaylist = "enable") result <- withVisible(func()) success <- TRUE }, finally = { if (!success) { getDims() } }) if (result$visible) { utils::capture.output({ plotResult <<- ..stacktraceon..(print(result$value)) }) } recordedPlot <<- grDevices::recordPlot() if (inherits(plotResult, "ggplot_build_gtable")) { coordmap <<- getGgplotCoordmap(plotResult, pixelratio, res) } else { coordmap <<- getPrevPlotCoordmap(dims$width, dims$height) }}, width = 629.999983310699, height = 629.999983310699, res = 64.7999982833862)
5: do.call(plotPNG, c(plotFunc, width = dims$width * pixelratio, height = dims$height * pixelratio, res = res * pixelratio, args))
6: ..stacktraceoff..(do.call(plotPNG, c(plotFunc, width = dims$width * pixelratio, height = dims$height * pixelratio, res = res * pixelratio, args)))
7: <reactive:plotObj>
(...)
8: ..stacktraceon..(<reactive:plotObj>
(...))
9: .func()
10: withVisible(.func())
11: withCallingHandlers({ .error <<- FALSE withVisible(.func())}, error = function(cond) { .value <<- cond .error <<- TRUE .visible <<- FALSE})
12: contextFunc()
13: env$runWith(self, func)
14: withReactiveDomain(.domain, { env <- .getReactiveEnvironment() .graphEnterContext(id) on.exit(.graphExitContext(id), add = TRUE) env$runWith(self, func)})
15: ctx$run(function() { result <- withCallingHandlers({ .error <<- FALSE withVisible(.func()) }, error = function(cond) { .value <<- cond .error <<- TRUE .visible <<- FALSE }) .value <<- result$value .visible <<- result$visible})
16: self$.updateValue()
17: ..stacktraceoff..(self$.updateValue())
18: plotObj()
19: origRenderFunc(...)
20: output$DEseqDispersionsPlot
(...)
21: ..stacktraceon..(output$DEseqDispersionsPlot
(...))
22: orig(name = name, shinysession = self)
23: func()
24: withCallingHandlers(expr, error = function(e) { if (is.null(attr(e, "stack.trace", exact = TRUE))) { calls <- sys.calls() attr(e, "stack.trace") <- calls stop(e) }})
25: captureStackTraces(expr)
26: withCallingHandlers(captureStackTraces(expr), error = function(e) { if (inherits(e, "shiny.silent.error")) return() handle <- getOption("shiny.error") if (is.function(handle)) handle()})
27: shinyCallingHandlers(func())
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
33: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
36: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
39: tryCatchList(expr, classes, parentenv, handlers)
40: tryCatch(shinyCallingHandlers(func()), shiny.custom.error = function(cond) { if (isTRUE(getOption("show.error.messages"))) printError(cond) structure(list(), class = "try-error", condition = cond)}, shiny.output.cancel = function(cond) { structure(list(), class = "cancel-output")}, shiny.silent.error = function(cond) { structure(list(), class = "try-error", condition = cond)}, error = function(cond) { if (isTRUE(getOption("show.error.messages"))) printError(cond) if (getOption("shiny.sanitize.errors", FALSE)) { cond <- simpleError(paste("An error has occurred. Check your", "logs or contact the app author for", "clarification.")) } invisible(structure(list(), class = "try-error", condition = cond))}, finally = { private$sendMessage(recalculating = list(name = name, status = "recalculated"))})
41: observerFunc()
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(expr, names, parentenv, handlers[[1L]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: tryCatch(if (..stacktraceon) ..stacktraceon..(observerFunc()) else observerFunc(), shiny.silent.error = function(e) NULL)
46: contextFunc()
47: env$runWith(self, func)
48: withReactiveDomain(.domain, { env <- .getReactiveEnvironment() .graphEnterContext(id) on.exit(.graphExitContext(id), add = TRUE) env$runWith(self, func)})
49: ctx$run(.func)
50: run()
51: withCallingHandlers(expr, error = function(e) { if (is.null(attr(e, "stack.trace", exact = TRUE))) { calls <- sys.calls() attr(e, "stack.trace") <- calls stop(e) }})
52: captureStackTraces(expr)
53: withCallingHandlers(captureStackTraces(expr), error = function(e) { if (inherits(e, "shiny.silent.error")) return() handle <- getOption("shiny.error") if (is.function(handle)) handle()})
54: shinyCallingHandlers(run())
55: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchOne(expr, names, parentenv, handlers[[1L]])
57: tryCatchList(expr, classes, parentenv, handlers)
58: tryCatch({ if (!.destroyed) shinyCallingHandlers(run())}, error = function(e) { printError(e) if (!is.null(.domain)) { .domain$unhandledError(e) }})
59: flushCallback()
60: FUN(X[[i]], ...)
61: lapply(.flushCallbacks, function(flushCallback) { flushCallback()})
62: ctx$executeFlushCallbacks()
63: .getReactiveEnvironment()$flush()
64: flushReact()
65: force(expr)
66: withRestoreContext(shinysession$restoreContext, { msg$data <- applyInputHandlers(msg$data) switch(msg$method, init = { serverFunc <- withReactiveDomain(NULL, serverFuncSource()) if (!identicalFunctionBodies(serverFunc, appvars$server)) { appvars$server <- serverFunc if (!is.null(appvars$server)) { attr(appvars$server, "shinyServerFunction") <- TRUE registerDebugHook("server", appvars, "Server Function") } } if (.globals$showcaseOverride && exists(".clientdata_url_search", where = msg$data)) { mode <- showcaseModeOfQuerystring(msg$data$.clientdata_url_search) if (!is.null(mode)) shinysession$setShowcase(mode) } shinysession$manageInputs(msg$data) if (!is.null(msg$data$.clientdata_singletons)) { shinysession$singletons <- strsplit(msg$data$.clientdata_singletons, ",")[[1]] } local({ args <- argsForServerFunc(serverFunc, shinysession) withReactiveDomain(shinysession, { do.call(wrapFunctionLabel(appvars$server, "server", ..stacktraceon = TRUE), args) }) }) }, update = { shinysession$manageInputs(msg$data) }, shinysession$dispatch(msg)) shinysession$manageHiddenOutputs() if (exists(".shiny__stdout", globalenv()) && exists("HTTP_GUID", ws$request)) { shiny_stdout <- get(".shiny__stdout", globalenv()) writeLines(paste("_n_flushReact ", get("HTTP_GUID", ws$request), " @ ", sprintf("%.3f", as.numeric(Sys.time())), sep = ""), con = shiny_stdout) flush(shiny_stdout) flushReact() writeLines(paste("_x_flushReact ", get("HTTP_GUID", ws$request), " @ ", sprintf("%.3f", as.numeric(Sys.time())), sep = ""), con = shiny_stdout) flush(shiny_stdout) } else { flushReact() } flushAllSessions()})
67: withReactiveDomain(shinysession, { if (is.character(msg)) msg <- charToRaw(msg) traceOption <- getOption("shiny.trace", FALSE) if (isTRUE(traceOption) || traceOption == "recv") { if (binary) message("RECV ", "$$binary data$$") else message("RECV ", rawToChar(msg)) } if (identical(charToRaw("\003\xe9"), msg)) return() msg <- decodeMessage(msg) if (is.null(shinysession$restoreContext)) { bookmarkStore <- getShinyOption("bookmarkStore", default = "disable") if (bookmarkStore == "disable") { shinysession$restoreContext <- RestoreContext$new() } else { shinysession$restoreContext <- RestoreContext$new(msg$data$.clientdata_url_search) } } withRestoreContext(shinysession$restoreContext, { msg$data <- applyInputHandlers(msg$data) switch(msg$method, init = { serverFunc <- withReactiveDomain(NULL, serverFuncSource()) if (!identicalFunctionBodies(serverFunc, appvars$server)) { appvars$server <- serverFunc if (!is.null(appvars$server)) { attr(appvars$server, "shinyServerFunction") <- TRUE registerDebugHook("server", appvars, "Server Function") } } if (.globals$showcaseOverride && exists(".clientdata_url_search", where = msg$data)) { mode <- showcaseModeOfQuerystring(msg$data$.clientdata_url_search) if (!is.null(mode)) shinysession$setShowcase(mode) } shinysession$manageInputs(msg$data) if (!is.null(msg$data$.clientdata_singletons)) { shinysession$singletons <- strsplit(msg$data$.clientdata_singletons, ",")[[1]] } local({ args <- argsForServerFunc(serverFunc, shinysession) withReactiveDomain(shinysession, { do.call(wrapFunctionLabel(appvars$server, "server", ..stacktraceon = TRUE), args) }) }) }, update = { shinysession$manageInputs(msg$data) }, shinysession$dispatch(msg)) shinysession$manageHiddenOutputs() if (exists(".shiny__stdout", globalenv()) && exists("HTTP_GUID", ws$request)) { shiny_stdout <- get(".shiny__stdout", globalenv()) writeLines(paste("_n_flushReact ", get("HTTP_GUID", ws$request), " @ ", sprintf("%.3f", as.numeric(Sys.time())), sep = ""), con = shiny_stdout) flush(shiny_stdout) flushReact() writeLines(paste("_x_flushReact ", get("HTTP_GUID", ws$request), " @ ", sprintf("%.3f", as.numeric(Sys.time())), sep = ""), con = shiny_stdout) flush(shiny_stdout) } else { flushReact() } flushAllSessions() })})
68: messageHandler(binary, msg)
69: withCallingHandlers(expr, error = function(e) { if (is.null(attr(e, "stack.trace", exact = TRUE))) { calls <- sys.calls() attr(e, "stack.trace") <- calls stop(e) }})
70: captureStackTraces(expr)
71: withCallingHandlers(captureStackTraces(expr), error = function(cond) { if (inherits(cond, "shiny.silent.error")) return() if (isTRUE(getOption("show.error.messages"))) { printError(cond, full = full, offset = offset) }})
72: withLogErrors(messageHandler(binary, msg))
73: handler(binary, message)
74: doTryCatch(return(expr), name, parentenv, handler)
75: tryCatchOne(expr, names, parentenv, handlers[[1L]])
76: tryCatchList(expr, classes, parentenv, handlers)
77: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
78: try(handler(binary, message))
79: (function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("44250960", FALSE, "{"method":"update","data":{".clientdata_output_DEseqDispersionsPlot_width":800,".clientdata_output_DEseqDispersionsPlot_height":0,".clientdata_output_DEseqMAplot_width":1097,".clientdata_output_DEseqMAplot_height":0,".clientdata_output_DESeqVolcanoPlotRender_width":1097,".clientdata_output_DESeqVolcanoPlotRender_height":0,".clientdata_output_DESeqheatmapRender_width":1097,".clientdata_output_DESeqheatmapRender_height":0,".clientdata_output_DESeqPvalueDistributionplotRender_width":1097,".clientdata_output_DESeqPvalueDistributionplotRender_height":0,".clientdata_output_DataInputswitchUI_hidden":true,".clientdata_output_designSwitchUI_hidden":true,".clientdata_output_interestvariablesUI_hidden":true,".clientdata_output_ConditionSelectionUI_hidden":true,".clientdata_output_DEseqTable_hidden":false,".clientdata_output_DESeqDisperplotDownload_hidden":false,".clientdata_output_DEseqDispersionsPlot_hidden":false,".clientdata_output_DEseqMAplotDownload_hidden":false,".clientdata_output_DEseqMAplot_hidden":false,".clientdata_output_normalizeFactor_hidden":false,".clientdata_output_DEseqVolcanoPlotDownload_hidden":false,".clientdata_output_DESeqVolcanoPlotRender_hidden":false,".clientdata_output_DESeqHeatmapDownload_hidden":false,".clientdata_output_DESeqheatmapRender_hidden":false,".clientdata_output_DESeqPvalueDistributionplotDownload_hidden":false,".clientdata_output_DESeqPvalueDistributionplotRender_hidden":false,".clientdata_output_comparisonSampleTextRenderUI2_hidden":false,".clientdata_output_DEseqdownloadDEtable_hidden":false,".clientdata_output_DownloadDESeqReport_hidden":false}}")
80: eval(substitute(expr), envir, enclos)
81: eval(substitute(expr), envir, enclos)
82: eval(substitute(expr), envir, enclos)
83: evalq((function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("44250960", FALSE, "{"method":"update","data":{".clientdata_output_DEseqDispersionsPlot_width":800,".clientdata_output_DEseqDispersionsPlot_height":0,".clientdata_output_DEseqMAplot_width":1097,".clientdata_output_DEseqMAplot_height":0,".clientdata_output_DESeqVolcanoPlotRender_width":1097,".clientdata_output_DESeqVolcanoPlotRender_height":0,".clientdata_output_DESeqheatmapRender_width":1097,".clientdata_output_DESeqheatmapRender_height":0,".clientdata_output_DESeqPvalueDistributionplotRender_width":1097,".clientdata_output_DESeqPvalueDistributionplotRender_height":0,".clientdata_output_DataInputswitchUI_hidden":true,".clientdata_output_designSwitchUI_hidden":true,".clientdata_output_interestvariablesUI_hidden":true,".clientdata_output_ConditionSelectionUI_hidden":true,".clientdata_output_DEseqTable_hidden":false,".clientdata_output_DESeqDisperplotDownload_hidden":false,".clientdata_output_DEseqDispersionsPlot_hidden":false,".clientdata_output_DEseqMAplotDownload_hidden":false,".clientdata_output_DEseqMAplot_hidden":false,".clientdata_output_normalizeFactor_hidden":false,".clientdata_output_DEseqVolcanoPlotDownload_hidden":false,".clientdata_output_DESeqVolcanoPlotRender_hidden":false,".clientdata_output_DESeqHeatmapDownload_hidden":false,".clientdata_output_DESeqheatmapRender_hidden":false,".clientdata_output_DESeqPvalueDistributionplotDownload_hidden":false,".clientdata_output_DESeqPvalueDistributionplotRender_hidden":false,".clientdata_output_comparisonSampleTextRenderUI2_hidden":false,".clientdata_output_DEseqdownloadDEtable_hidden":false,".clientdata_output_DownloadDESeqReport_hidden":false}}"), )
84: doTryCatch(return(expr), name, parentenv, handler)
85: tryCatchOne(expr, names, parentenv, handlers[[1L]])
86: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
87: doTryCatch(return(expr), name, parentenv, handler)
88: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
89: tryCatchList(expr, classes, parentenv, handlers)
90: tryCatch(evalq((function (handle, binary, message) { for (handler in .wsconns[[as.character(handle)]]$.messageCallbacks) { result <- try(handler(binary, message)) if (inherits(result, "try-error")) { .wsconns[[as.character(handle)]]$close() return() } }})("44250960", FALSE, "{"method":"update","data":{".clientdata_output_DEseqDispersionsPlot_width":800,".clientdata_output_DEseqDispersionsPlot_height":0,".clientdata_output_DEseqMAplot_width":1097,".clientdata_output_DEseqMAplot_height":0,".clientdata_output_DESeqVolcanoPlotRender_width":1097,".clientdata_output_DESeqVolcanoPlotRender_height":0,".clientdata_output_DESeqheatmapRender_width":1097,".clientdata_output_DESeqheatmapRender_height":0,".clientdata_output_DESeqPvalueDistributionplotRender_width":1097,".clientdata_output_DESeqPvalueDistributionplotRender_height":0,".clientdata_output_DataInputswitchUI_hidden":true,".clientdata_output_designSwitchUI_hidden":true,".clientdata_output_interestvariablesUI_hidden":true,".clientdata_output_ConditionSelectionUI_hidden":true,".clientdata_output_DEseqTable_hidden":false,".clientdata_output_DESeqDisperplotDownload_hidden":false,".clientdata_output_DEseqDispersionsPlot_hidden":false,".clientdata_output_DEseqMAplotDownload_hidden":false,".clientdata_output_DEseqMAplot_hidden":false,".clientdata_output_normalizeFactor_hidden":false,".clientdata_output_DEseqVolcanoPlotDownload_hidden":false,".clientdata_output_DESeqVolcanoPlotRender_hidden":false,".clientdata_output_DESeqHeatmapDownload_hidden":false,".clientdata_output_DESeqheatmapRender_hidden":false,".clientdata_output_DESeqPvalueDistributionplotDownload_hidden":false,".clientdata_output_DESeqPvalueDistributionplotRender_hidden":false,".clientdata_output_comparisonSampleTextRenderUI2_hidden":false,".clientdata_output_DEseqdownloadDEtable_hidden":false,".clientdata_output_DownloadDESeqReport_hidden":false}}"), ), error = function (x) x, interrupt = function (x) x)
91: .Call("httpuv_run", PACKAGE = "httpuv", timeoutMillis)
92: run(timeoutMs)
93: service(timeout)
94: serviceApp()
95: withCallingHandlers(expr, error = function(e) { if (is.null(attr(e, "stack.trace", exact = TRUE))) { calls <- sys.calls() attr(e, "stack.trace") <- calls stop(e) }})
96: captureStackTraces({ scheduleFlush() while (!.globals$stopped) { serviceApp() Sys.sleep(0.001) }})
97: ..stacktraceoff..(captureStackTraces({ scheduleFlush() while (!.globals$stopped) { serviceApp() Sys.sleep(0.001) }}))
98: shiny::runApp(system.file("IDEA", package = "IDEA"))
99: runIDEA()
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Hi there,
I have a data with 4 conditions and have the matrix of experimental design, when I run DESeq2 to compare condition1 to condition4 and condition 2 to condtion4 both shows the same result, while edgeR gives different results for same analysis, I think DESeq2 script has some problem, can you please rectify it?
Thanks
Pradyumna
hello,
I would like to suggest that it would be helpful if the output file names are saved in the name of condition instead of time and date. like currently output name for deseq analysis is like DEseqDEresult2017-03-07 22-09-12.csv
instead if it is like DEseqDEresultCondition1vsCondition2.csv
it will be easy to differentiate the files.
When I change the Ensembl id to gene names in my input data the analysis stops giving following error
Error:non-numeric argument to mathematical function
Is there any way to overcome this? providing facility to use gene names would be more helpful.
Thank you
Pradyumna
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A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.