Hello all,
I have been trying to use cummeRbund for a long time but I have not been able to get the graphics (plots) to show up either by "windows()" or by making a pdf file.  I am using R on windows.  I am pretty new to R so I am not sure if this is a general R issue or some issue specific to this package.  I have been able to generate plots in other packages...  This is the code that I used:

>install.packages("RSQLite")
>install.packages("ggplot2")
>install.packages("reshape2")
>install.packages("plyr")
>install.packages("fastcluster")
>source("http://bioconductor.org/biocLite.R")
>biocLite("rtracklayer")
>biocLite("Gviz")
>biocLite("cummeRbund")
> setwd("C:/Users/jtoman01/Desktop/RNA Seq/combinedsexcuffdiff7.24")
> cuff_data <- readCufflinks()
> annot <- read.table("gene_exp.diff",sep="\t",header=T,na.string="-")
> addFeatures(cuff_data,annot,level="genes")
> windows()
> disp<-dispersionPlot(genes(cuff_data))
> pdf("dispersion.pdf")
> disp<-dispersionPlot(genes(cuff_data))
> dev.off()

As far as warnings or errors, this was the only thing, which showed up after "cuff_data <- readCufflinks()":
Warning messages:
1: attributes are not identical across measure variables; they will be dropped
2: attributes are not identical across measure variables; they will be dropped
3: attributes are not identical across measure variables; they will be dropped
4: attributes are not identical across measure variables; they will be dropped
5: attributes are not identical across measure variables; they will be dropped
6: attributes are not identical across measure variables; they will be dropped
7: attributes are not identical across measure variables; they will be dropped
8: attributes are not identical across measure variables; they will be dropped

Here is my sessionInfo():
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] cummeRbund_2.6.1     Gviz_1.8.4           rtracklayer_1.24.2   GenomicRanges_1.16.3 GenomeInfoDb_1.0.2   IRanges_1.22.9
 [7] BiocGenerics_0.10.0  fastcluster_1.1.13   plyr_1.8.1           reshape2_1.4         ggplot2_1.0.0        RSQLite_0.11.4
[13] DBI_0.2-7            BiocInstaller_1.14.2

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.26.0     BatchJobs_1.3            BBmisc_1.7               Biobase_2.24.0           BiocParallel_0.6.1
 [6] biomaRt_2.20.0           Biostrings_2.32.1        biovizBase_1.12.1        bitops_1.0-6             brew_1.0-6
[11] BSgenome_1.32.0          checkmate_1.2            cluster_1.15.2           codetools_0.2-8          colorspace_1.2-4
[16] dichromat_2.0-0          digest_0.6.4             fail_1.2                 foreach_1.4.2            Formula_1.1-2
[21] GenomicAlignments_1.0.3  GenomicFeatures_1.16.2   gtable_0.1.2             Hmisc_3.14-4             iterators_1.0.7
[26] lattice_0.20-29          latticeExtra_0.6-26      MASS_7.3-33              matrixStats_0.10.0       munsell_0.4.2
[31] proto_0.3-10             R.methodsS3_1.6.1        RColorBrewer_1.0-5       Rcpp_0.11.2              RCurl_1.95-4.1
[36] Rsamtools_1.16.1         scales_0.2.4             sendmailR_1.1-2          splines_3.1.1            stats4_3.1.1
[41] stringr_0.6.2            survival_2.37-7          tools_3.1.1              VariantAnnotation_1.10.5 XML_3.98-1.1
[46] XVector_0.4.0            zlibbioc_1.10.0

Could someone please help me figure out how to generate these graphics?
Thank you very much!!
Best,
Julia




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