[BioC] error on detecting regions

guest [guest] guest at bioconductor.org
Tue Jun 17 23:30:43 CEST 2014

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:
postAcute <- Mset.postAcute$Stage
pre <- Mset.pre$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)

[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       

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