Hi Camille, I'm not sure about this error. You could try reinstalling DESeq? Also, we recommend using DESeq2, which is available as a separate Bioconductor package: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html Mike On May 4, 2014 5:15 PM, "Camille BENOIST" <camil.benoist@gmail.com> wrote: > I just saw another warning: > when R starts, I can read at the end: > > Warning: namespace ‘DESeq’ is not available and has been replaced by > .GlobalEnv when processing object ‘cds’ > > Ragards, > > Camille Benoist > > > 2014-05-04 18:20 GMT+02:00 Benoist [guest] <guest@bioconductor.org>: > > > > > Dear Madam or Sir, > > > > I am a post-doctorant working on NGS data (from ChIP seq to RNAseq) but I > > have problems when I use DESeq for differential analysis. When I want to > > estimate dispersion I have this error message: > > "Error in FUN(newX[, i], ...) : could not find function "locfunc" > > > > Here is an example of the problem : > > > > # first I just load a matrix of 20000 rows and I select 8 columns > > > data = read.csv("H3K27me3-ensembl-59-gene-bodies-counts.txt", sep="\t") > > > cols = c(grep("BN", colnames(data)), grep("SHR", colnames(data))) > > > data=data[,cols] > > > head(data) > > liver.H3K27me3.BN.male.bio1 > liver.H3K27me3.BN.male.bio2 > > liver.H3K27me3.BN.male.bio3 liver.H3K27me3.BN.male.bio4 > > ENSRNOG00000005665 3 > 3 > > 11 11 > > ENSRNOG00000023458 99 > 74 > > 105 104 > > ENSRNOG00000031533 56 > 34 > > 48 36 > > ENSRNOG00000032223 0 > 1 > > 0 0 > > ENSRNOG00000040189 0 > 0 > > 0 0 > > ENSRNOG00000005894 3496 > 3874 > > 3657 4008 > > liver.H3K27me3.SHR.male.bio1 > > liver.H3K27me3.SHR.male.bio2 liver.H3K27me3.SHR.male.bio3 > > ENSRNOG00000005665 2 > > 6 5 > > ENSRNOG00000023458 41 > > 113 110 > > ENSRNOG00000031533 19 > > 52 50 > > ENSRNOG00000032223 1 > > 2 1 > > ENSRNOG00000040189 0 > > 0 0 > > ENSRNOG00000005894 1588 > > 2990 3058 > > liver.H3K27me3.SHR.male.bio4 > > ENSRNOG00000005665 9 > > ENSRNOG00000023458 99 > > ENSRNOG00000031533 47 > > ENSRNOG00000032223 0 > > ENSRNOG00000040189 0 > > ENSRNOG00000005894 3732 > > > > # then I use DESeq to perform a differential analysis > > > library(DESeq) > > 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 object is masked from ‘package:stats’: > > > > xtabs > > > > The following objects are masked from ‘package:base’: > > > > anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, > > do.call, duplicated, eval, evalq, Filter, Find, > > get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, > > paste, pmax, pmax.int, pmin, pmin.int, > > Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, > > sort, table, tapply, union, unique, unlist > > > > 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")'. > > > > Loading required package: locfit > > locfit 1.5-9.1 2013-03-22 > > Loading required package: lattice > > Welcome to 'DESeq'. For improved performance, usability and > > functionality, please consider migrating to 'DESeq2'. > > > > > > > strain = factor(rep(c("BN", "SHR"), each=4)) > > > cds = newCountDataSet(data, strain) > > > cds=estimateSizeFactors(cds) > > Error in FUN(newX[, i], ...) : could not find function "locfunc" > > > > > > > traceback() > > 6: FUN(newX[, i], ...) > > 5: apply(counts, 2, function(cnts) exp(locfunc((log(cnts) - > > loggeomeans)[is.finite(loggeomeans)]))) > > 4: estimateSizeFactorsForMatrix(counts(object), locfunc) > > 3: .local(object, ...) > > 2: estimateSizeFactors(cds) > > 1: estimateSizeFactors(cds) > > > ?locfunc > > No documentation for ‘locfunc’ in specified packages and libraries: > > you could try ‘??locfunc’ > > > > > > I already try to find an answer by copy and past this error message on > > google but I didn't find anything. > > So I have follow bioconductor advice, I install R again, DESeq again, I > > check if the package were up to date... but after that nothing change, > > there is still this error message. > > The thing is : I never had this problem with my previous computer when I > > was performing such analysis on such kind of data. > > > > Thank you for any halp you could provide! > > > > Camille BENOIST > > > > -- output of sessionInfo(): > > > > R version 3.1.0 (2014-04-10) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 > > LC_MONETARY=French_France.1252 LC_NUMERIC=C > > [5] LC_TIME=French_France.1252 > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets methods > > base > > > > other attached packages: > > [1] DESeq_1.16.0 lattice_0.20-29 locfit_1.5-9.1 > > Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > > > loaded via a namespace (and not attached): > > [1] annotate_1.42.0 AnnotationDbi_1.26.0 DBI_0.2-7 > > genefilter_1.46.0 geneplotter_1.42.0 GenomeInfoDb_1.0.2 > > [7] grid_3.1.0 IRanges_1.22.6 RColorBrewer_1.0-5 > > RSQLite_0.11.4 splines_3.1.0 stats4_3.1.0 > > [13] survival_2.37-7 tools_3.1.0 XML_3.98-1.1 > > xtable_1.7-3 > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]