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Warning: namespace ‘DESeq’ is not available and has been replaced by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.
>

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