Hi, I ran into an error when trying to do limma using this line:

fit <- lmFit(eset, design)

Then this error appeared:

Error in as.vector(data) : 
  no method for coercing this S4 class to a vector. Can someone help?

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] oligo_1.30.0          Biostrings_2.34.1     XVector_0.6.0         oligoClasses_1.28.0   RColorBrewer_1.1-2  
[6] geneplotter_1.44.0    annotate_1.44.0       XML_3.98-1.2          annaffy_1.38.0        KEGG.db_3.0.0       
[11] affyQCReport_1.44.0   lattice_0.20-31       affycoretools_1.38.0  GO.db_3.0.0           RSQLite_1.0.0       
[16] DBI_0.3.1             AnnotationDbi_1.28.2  GenomeInfoDb_1.2.5    IRanges_2.0.1         S4Vectors_0.4.0     
[21] simpleaffy_2.42.0     genefilter_1.48.1     limma_3.22.7          affyPLM_1.42.0        preprocessCore_1.28.0
[26] gcrma_2.38.0          affydata_1.13.1       affy_1.44.0           Biobase_2.26.0        BiocGenerics_0.12.1  

loaded via a namespace (and not attached):
[1] acepack_1.3-3.3           affxparser_1.38.0         affyio_1.34.0             AnnotationForge_1.8.2   
[5] base64enc_0.1-2           BatchJobs_1.6             BBmisc_1.9                BiocInstaller_1.16.5    
[9] BiocParallel_1.0.3        biomaRt_2.22.0            biovizBase_1.14.1         bit_1.1-12              
[13] bitops_1.0-6              brew_1.0-6                BSgenome_1.34.1           Category_2.32.0         
[17] caTools_1.17.1            checkmate_1.6.0           cluster_2.0.2             codetools_0.2-11        
[21] colorspace_1.2-6          DESeq2_1.6.3              dichromat_2.0-0           digest_0.6.8            
[25] edgeR_3.8.6               fail_1.2                  ff_2.2-13                 foreach_1.4.2           
[29] foreign_0.8-63            Formula_1.2-1             gdata_2.16.1              GenomicAlignments_1.2.2 
[33] GenomicFeatures_1.18.7    GenomicRanges_1.18.4      GGally_0.5.0              ggbio_1.14.0            
[37] ggplot2_1.0.1             GOstats_2.32.0            gplots_2.17.0             graph_1.44.1            
[41] grid_3.1.3                gridExtra_0.9.1           GSEABase_1.28.0           gtable_0.1.2            
[45] gtools_3.4.2              Hmisc_3.16-0              hwriter_1.3.2             iterators_1.0.7         
[49] KernSmooth_2.23-14        knitr_1.10.5              latticeExtra_0.6-26       locfit_1.5-9.1          
[53] magrittr_1.5              MASS_7.3-41               Matrix_1.2-1              munsell_0.4.2           
[57] nnet_7.3-9                OrganismDbi_1.8.1         PFAM.db_3.0.0             plyr_1.8.3              
[61] proto_0.3-10              R.methodsS3_1.7.0         R.oo_1.19.0               R.utils_2.1.0           
[65] RBGL_1.42.0               Rcpp_0.11.6               RcppArmadillo_0.5.200.1.0 RCurl_1.95-4.6          
[69] ReportingTools_2.6.0      reshape_0.8.5             reshape2_1.4.1            rpart_4.1-9             
[73] Rsamtools_1.18.3          rtracklayer_1.26.3        scales_0.2.5              sendmailR_1.2-1         
[77] splines_3.1.3             stringi_0.5-2             stringr_1.0.0             survival_2.38-2         
[81] tools_3.1.3               VariantAnnotation_1.12.9  xtable_1.7-4              zlibbioc_1.12.0         

Thanks much, Wing

My guess is that this error has nothing to do limma or with Yosemite. My suspicion is that one of the many other packages you have loaded or imported is misbehaving and has perhaps redefined as.vector() in an unhelpful way. To confirm this, try loading limma by itself and running the code again. This sort of problem has occurred before, see A: barcode plot function in limma

BTW, the posting guide asks you to use the current release versions of R and Bioconductor. The current versions are R 3.2.1 and limma 3.24.12.

Thanks for the answer, I will definitely follow your advice. The reason I used the older version was that I could not get limma to work in the latest version.

Best, Wing