Hi

Please update your R and methyAnalysis package to the latest released
versions (R 3.1.0, methyAnalysis 1.6.0), and send me the error messages and
related data if it still happens.
Thanks!

Pan



On Tue, Jun 17, 2014 at 2:30 PM, guest [guest] <guest@bioconductor.org>
wrote:

> Dear Users,
>
> I met an error that struggled me really long time to figure out. I tried
> to use detectDMR.slideWin() function, but no matter how I change the
> factors assign to sampleType, it still has the error.
>
> I have several different conditions in a factor - Stage (PRE, POST-ACUTE,
> POST-COL and POST-LAT). I would like to compare POST-ACUTE with PRE.
>
> Here are script:
> Mset.postAcute=Mset[,Mset$Stage=='POST-ACUTE']
> postAcute <- Mset.postAcute$Stage
> Mset.pre=Mset[,Mset$Stage=='PRE']
> pre <- Mset.pre$Stage
>
> ResultStage <- detectDMR.slideWin(Mset, sampleType=c(postAcute, pre))
>
> Error message:
> Error in rowcoltt(x, fac, tstatOnly, 1L) :
>   length(fac)=42, ncol(x)=80, should be the same.
> In addition: Warning messages:
> 1: Please use rownames. We are switching away from eSet-specific methods.
> 2: Please use colnames. We are switching away from eSet-specific methods.
> 3: Please use rownames. We are switching away from eSet-specific methods.
> 4: Please use colnames. We are switching away from eSet-specific methods.
>
>
>  -- output of sessionInfo():
>
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      parallel  stats     graphics  grDevices utils     datasets
>  methods   base
>
> other attached packages:
>  [1] FDb.InfiniumMethylation.hg19_2.0.10
> BSgenome.Hsapiens.UCSC.hg19_1.3.19  BSgenome_1.30.0
> GenomicFeatures_1.14.5
>  [5] methyAnalysis_1.4.2                 org.Hs.eg.db_2.10.1
>   RSQLite_0.11.4                      DBI_0.2-7
>  [9] AnnotationDbi_1.24.0                lumi_2.14.2
>   BiocInstaller_1.12.1                VariantAnnotation_1.8.13
> [13] Rsamtools_1.14.3                    Biostrings_2.30.1
>   GenomicRanges_1.14.4                XVector_0.2.0
> [17] IRanges_1.20.7                      ggplot2_1.0.0
>   phyloseq_1.6.1                      picante_1.6-2
> [21] nlme_3.1-117                        ape_3.1-2
>   ade4_1.6-2                          knitr_1.6
> [25] vegan_2.0-10                        lattice_0.20-29
>   permute_0.8-3                       biom_0.3.12
> [29] metagenomeSeq_1.5.47                devtools_1.5
>    gplots_2.13.0                       RColorBrewer_1.0-5
> [33] matrixStats_0.10.0                  limma_3.18.13
>   Biobase_2.22.0                      BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
>  [1] affy_1.40.0           affyio_1.30.0         annotate_1.40.1
> base64_1.1            beanplot_1.1          biomaRt_2.18.0
>  [7] biovizBase_1.10.8     bitops_1.0-6          bumphunter_1.2.0
>  caTools_1.17          cluster_1.15.2        codetools_0.2-8
> [13] colorspace_1.2-4      dichromat_2.0-0       digest_0.6.4
>  doRNG_1.6             evaluate_0.5.5        foreach_1.4.2
> [19] formatR_0.10          Formula_1.1-1         gdata_2.13.3
>  genefilter_1.44.0     genoset_1.14.0        gtable_0.1.2
> [25] gtools_3.4.1          Gviz_1.6.0            Hmisc_3.14-4
>  httr_0.3              igraph_0.7.1          illuminaio_0.4.0
> [31] iterators_1.0.7       itertools_0.1-3       KernSmooth_2.23-12
>  labeling_0.2          latticeExtra_0.6-26   locfit_1.5-9.1
> [37] MASS_7.3-33           Matrix_1.1-4          mclust_4.3
>  memoise_0.2.1         methylumi_2.8.0       mgcv_1.7-29
> [43] minfi_1.8.9           multtest_2.18.0       munsell_0.4.2
> nleqslv_2.2           nor1mix_1.1-4         pkgmaker_0.22
> [49] plyr_1.8.1            preprocessCore_1.24.0 proto_0.3-10
>  R.methodsS3_1.6.1     Rcpp_0.11.2           RCurl_1.95-4.1
> [55] registry_0.2          reshape_0.8.5         reshape2_1.4
>  RJSONIO_1.2-0.2       rngtools_1.2.4        rtracklayer_1.22.7
> [61] scales_0.2.4          siggenes_1.36.0       splines_3.0.2
> stats4_3.0.2          stringr_0.6.2         survival_2.37-7
> [67] tools_3.0.2           whisker_0.3-2         XML_3.95-0.2
>  xtable_1.7-3          zlibbioc_1.8.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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