Entering edit mode
Hi All,
I got illegal operation when I run DEXSeq.
May I know the possible reasons for this error?
Follows are outputs of log file:
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
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> load('DEXseq.RData')
> library(DEXSeq)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ?BiocGenerics?
The following object(s) are masked from ?package:stats?:
xtabs
The following object(s) are masked from ?package:base?:
anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> ecs <- estimateDispersions(ecs)
*** caught illegal operation ***
address 0x2b101e337220, cause 'illegal operand'
Traceback:
1: drop(exp(X %*% beta + offset))
2: glmnb.fit(mm, y, initialGuess, mf$offset, coef.start = start)
3: fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, coef.start
= start))
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: 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 = stderr())
.Internal(printDeferredWarnings()) } invisible(structure(msg,
class = "try-error", condition = e))})
8: try(fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset,
coef.start = start)), silent = TRUE)
9: FUN(c("ENSMUSG00000073295", "ENSMUSG00000073293",
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"ENSMUSG00000053916", "ENSMUSG00000082809", "ENSMUSG00000027455",
"ENSMUSG00000087433", "ENSMUSG00000032966", "ENSMUSG00000027456",
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"ENSMUSG00000032852", "ENSMUSG00000086620", "ENSMUSG00000027460",
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"ENSMUSG00000032680", "ENSMUSG00000000359", "ENSMUSG00000019188",
"ENSMUSG00000097722", "ENSMUSG00000042745", "ENSMUSG00000009876",
"ENSMUSG00000007659", "ENSMUSG00000027469", "ENSMUSG00000027470",
"ENSMUSG00000042662", "ENSMUSG00000074673", "ENSMUSG00000089898",
"ENSMUSG00000027472", "ENSMUSG00000027474", "ENSMUSG00000003283",
"ENSMUSG00000068040", "ENSMUSG00000051413", "ENSMUSG00000046020",
"ENSMUSG00000027475", "ENSMUSG00000073236", "ENSMUSG00000042548",
"ENSMUSG00000061411", "ENSMUSG00000056941", "ENSMUSG00000027478",
"ENSMUSG00000082079", "ENSMUSG00000027479", "ENSMUSG00000044083",
"ENSMUSG00000083097", "ENSMUSG00000067998", "ENSMUSG00000027487",
"ENSMUSG00000027488", "ENSMUSG00000038533", "ENSMUSG00000027489",
"ENSMUSG00000038523", "ENSMUSG00000027490", "ENSMUSG00000000876",
"ENSMUSG00000059842", "ENSMUSG00000085483", "ENSMUSG00000038467",
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"ENSMUSG00000084897", "ENSMUSG00000027597", "ENSMUSG00000027598",
"ENSMUSG00000047459", "ENSMUSG00000027602", "ENSMUSG00000038383",
"ENSMUSG00000038375", "ENSMUSG00000038369", "ENSMUSG00000080237",
"ENSMUSG00000027603", "ENSMUSG00000027605", "ENSMUSG00000086529",
"ENSMUSG00000027610", "ENSMUSG00000085317", "ENSMUSG00000074652",
"ENSMUSG00000038324", "ENSMUSG00000038312", "ENSMUSG00000027611",
"ENSMUSG00000027612", "ENSMUSG00000074649", "ENSMUSG00000027613",
"ENSMUSG00000086754", "ENSMUSG00000074647", "ENSMUSG00000005882",
"ENSMUSG00000038259", "ENSMUSG00000074646", "ENSMUSG00000005881",
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"ENSMUSG00000061689", "ENSMUSG00000086638", "ENSMUSG00000067818",
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"ENSMUSG00000055485", "ENSMUSG00000027639", "ENSMUSG00000027641",
"ENSMUSG00000074627", "ENSMUSG00000027642", "ENSMUSG00000063019",
"ENSMUSG00000027646", "ENSMUSG00000081740", "ENSMUSG00000087445",
"ENSMUSG00000067787", "ENSMUSG00000067786", "ENSMUSG00000087547",
"ENSMUSG00000027649", "ENSMUSG00000062846", "ENSMUSG00000027650",
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"ENSMUSG00000044349", "ENSMUSG00000027652", "ENSMUSG00000037761",
"ENSMUSG00000027654", "ENSMUSG00000027655", "ENSMUSG00000070544",
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"ENSMUSG00000017817", "ENSMUSG00000035399", "ENSMUSG00000017943",
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"ENSMUSG00000017652", "ENSMUSG00000017664", "ENSMUSG00000017670",
"ENSMUSG00000017667", "ENSMUSG00000027670", "ENSMUSG00000018459",
"ENSMUSG00000039725", "ENSMUSG00000027661", "ENSMUSG00000017897",
"ENSMUSG00000085274", "ENSMUSG00000086820", "ENSMUSG00000087351",
"ENSMUSG00000027678", "ENSMUSG00000006800", "ENSMUSG00000039621",
"ENSMUSG00000042854", "ENSMUSG00000074582", "ENSMUSG00000002718",
"ENSMUSG00000090397", "ENSMUSG00000039536", "ENSMUSG00000082665",
"ENSMUSG00000017999", "ENSMUSG00000039501", "ENSMUSG00000074578",
"ENSMUSG00000086605", "ENSMUSG00000050556", "ENSMUSG00000085151",
"ENSMUSG00000017969", "ENSMUSG00000017929", "ENSMUSG00000039463",
"ENSMUSG00000047030", "ENSMUSG00000006418", "ENSMUSG00000042821",
"ENSMUSG00000085596", "ENSMUSG00000078923", "ENSMUSG00000089739",
"ENSMUSG00000090213", "ENSMUSG00000085914", "ENSMUSG00000006462",
"ENSMUSG00000084797", "ENSMUSG00000087624", "ENSMUSG00000087684",
"ENSMUSG00000027540", "ENSMUSG00000074577", "ENSMUSG00000044641",
"ENSMUSG00000093752", "ENSMUSG00000051149", "ENSMUSG00000078919",
"ENSMUSG00000074575", "ENSMUSG00000027544", "ENSMUSG00000027546",
"ENSMUSG00000027551", "ENSMUSG00000052368", "ENSMUSG00000047907",
"ENSMUSG00000096972", "ENSMUSG00000052056", "ENSMUSG00000052033",
"ENSMUSG00000085495", "ENSMUSG00000027560", "ENSMUSG00000085949",
"ENSMUSG00000027495", "ENSMUSG00000027496", "ENSMUSG00000027498",
"ENSMUSG00000074570", "ENSMUSG00000027502", "ENSMUSG00000074569",
"ENSMUSG00000027505", "ENSMUSG00000081344", "ENSMUSG00000028640",
"ENSMUSG00000027509", "ENSMUSG00000027510", "ENSMUSG00000092596",
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"ENSMUSG00000038400", "ENSMUSG00000087600", "ENSMUSG00000055897",
"ENSMUSG00000027519", "ENSMUSG00000054455", "ENSMUSG00000027522",
"ENSMUSG00000039263", "ENSMUSG00000086537", "ENSMUSG00000027523",
"ENSMUSG00000090625", "ENSMUSG00000016253", "ENSMUSG00000016256",
"ENSMUSG00000016252", "ENSMUSG00000016257", "ENSMUSG00000078906",
"ENSMUSG00000078905", "ENSMUSG00000084050", "ENSMUSG00000080888",
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"ENSMUSG00000083481", "ENSMUSG00000086941", "ENSMUSG00000078887",
"ENSMUSG00000089756", "ENSMUSG00000078886", "ENSMUSG00000078891",
"ENSMUSG00000085103", "ENSMUSG00000095648", "ENSMUSG00000086367",
"ENSMUSG00000078894", "ENSMUSG00000094108", "ENSMUSG00000084858",
"ENSMUSG00000078895", "ENSMUSG00000089951", "ENSMUSG00000078881",
"ENSMUSG00000095199", "ENSMUSG00000078880", "ENSMUSG00000078879",
"ENSMUSG00000078878", "ENSMUSG00000081599", "ENSMUSG00000078877",
"ENSMUSG00000078876", "ENSMUSG00000083170", "ENSMUSG00000074527",
"ENSMUSG00000094193", "ENSMUSG00000081326", "ENSMUSG00000078875",
"ENSMUSG00000083317", "ENSMUSG00000083111", "ENSMUSG00000078872",
"ENSMUSG00000082765", "ENSMUSG00000082724", "ENSMUSG00000081590",
"ENSMUSG00000078870", "ENSMUSG00000083817", "ENSMUSG00000078869",
"ENSMUSG00000078868", "ENSMUSG00000078867", "ENSMUSG00000082343",
"ENSMUSG00000078866", "ENSMUSG00000094786", "ENSMUSG00000078865",
"ENSMUSG00000080709", "ENSMUSG00000078864", "ENSMUSG00000095362",
"ENSMUSG00000081574", "ENSMUSG00000074521", "ENSMUSG00000074529",
"ENSMUSG00000078862", "ENSMUSG00000074519", "ENSMUSG00000097879",
"ENSMUSG00000078861", "ENSMUSG00000027525", "ENSMUSG00000060445",
"ENSMUSG00000070476", "ENSMUSG00000039155", "ENSMUSG00000000305",
"ENSMUSG00000039117", "ENSMUSG00000085704", "ENSMUSG00000039108",
"ENSMUSG00000027566", "ENSMUSG00000039086", "ENSMUSG00000039069",
"ENSMUSG00000039050", "ENSMUSG00000039041", "ENSMUSG00000039001",
"ENSMUSG00000038990", "ENSMUSG00000084843", "ENSMUSG00000038963",
"ENSMUSG00000027568", "ENSMUSG00000027569", "ENSMUSG00000049401",
"ENSMUSG00000027570", "ENSMUSG00000038932", "ENSMUSG00000038914",
"ENSMUSG00000027573", "ENSMUSG00000023393", "ENSMUSG00000038848",
"ENSMUSG00000027574", "ENSMUSG00000027575", "ENSMUSG00000016356",
"ENSMUSG00000027577", "ENSMUSG00000016349", "ENSMUSG00000016344",
"ENSMUSG00000047841", "ENSMUSG00000027580", "ENSMUSG00000038705",
"ENSMUSG00000084033", "ENSMUSG00000038671", "ENSMUSG00000027582",
"ENSMUSG00000090077", "ENSMUSG00000085028", "ENSMUSG00000027583",
"ENSMUSG00000000827", "ENSMUSG00000000826", "ENSMUSG00000089917",
"ENSMUSG00000010492", "ENSMUSG00000000823", "ENSMUSG00000002455",
"ENSMUSG00000038605", "ENSMUSG00000059540", "ENSMUSG00000002458",
"ENSMUSG00000027584", "ENSMUSG00000027589", "ENSMUSG00000038628",
"ENSMUSG00000096438", "ENSMUSG00000095134",
"ENSMUSG00000096768")[[1L]], ...)
10: lapply(testablegenes, function(gn) { y <-
modelFrames[[gn]]$count y1 <- pmax(y, 1/6) mf <-
modelFrames[[gn]] mm <- modelmatrices[[gn]] fit <- lm.fit(mm,
log(y1) - mf$offset) mm <- mm[, !is.na(fit$coefficients)] if
(nrow(mm) <= ncol(mm)) stop("Underdetermined model; cannot
estimate dispersions. Maybe replicates have not been properly
specified.") start <- fit$coefficients[!is.na(fit$coefficients)]
muhat <- try(fitted.values(glmnb.fit(mm, y, initialGuess,
mf$offset, coef.start = start)), silent = TRUE) muhat})
11: .local(object, ...)
12: estimateDispersions(ecs)
13: estimateDispersions(ecs)
aborting ...
Yours sincerely,
Jianhong Ou
jianhong.ou at umassmed.edu