Hello I was wondering if anyone can help. I have a 4 group exposure for my methylation array experiments, groups one, two, three and four I have used: plotDMRs(dmrs=thedmrs, Genome=Hsapiens, cpg.islands=cpg.cur, exposure=pd$tissue,outfile="./group1-group2.pdf", which_plot=c(1),which_points=c("group1","group2"), smoo="loess", ADD=3000,cols=c("black","red","blue")) To try and plot Group 1 against group 2. However I get: Error: length(cols) >= length(unique(exposure)) is not TRUE I am using the following to generate the DMRs, and finds 125 DMRs: thedmrs = dmrFind(p=p, mod=mod, mod0=mod0, coeff=2, pns=pns, chr=chr, pos=pos) And the output I get is: Running SVA Number of significant surrogate variables is: 10 Iteration (out of 5 ):1 2 3 4 5 Regression Obtaining estimates for factor(pd$tissue, levels = c("group1", "group2", "group3", "group4"))group2 Smoothing ====================================================================== ========== ................................................... Covariate recognized as categorical. Found 125 potential DMRs Can anyone help? -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] corpcor_1.6.4 BSgenome.Hsapiens.UCSC.hg18_1.3.19 [3] BSgenome_1.26.1 Biostrings_2.26.2 [5] GenomicRanges_1.10.3 IRanges_1.16.4 [7] pd.2006.11.02.hg18.cpg.promo_0.0.1 oligo_1.22.0 [9] oligoClasses_1.20.0 RSQLite_0.11.2 [11] DBI_0.2-5 charm_2.4.0 [13] genefilter_1.40.0 RColorBrewer_1.0-5 [15] fields_6.7 spam_0.29-2 [17] SQN_1.0.5 nor1mix_1.1-3 [19] mclust_4.0 Biobase_2.18.0 [21] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.30.0 affyio_1.26.0 annotate_1.36.0 [4] AnnotationDbi_1.20.2 BiocInstaller_1.8.3 bit_1.1-9 [7] codetools_0.2-8 ff_2.2-9 foreach_1.4.0 [10] gtools_2.7.0 iterators_1.0.6 limma_3.14.1 [13] MASS_7.3-22 multtest_2.14.0 parallel_2.15.2 [16] preprocessCore_1.20.0 siggenes_1.32.0 splines_2.15.2 [19] stats4_2.15.2 survival_2.36-14 sva_3.4.0 [22] tools_2.15.2 XML_3.95-0.1 xtable_1.7-0 [25] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

Okay I have solved the problem, sorry I was stupid! Didn't realise I needed to specify four colours for the four regions! BW Andrew -----Original Message----- From: Andrew Beggs [guest] [mailto:guest@bioconductor.org] Sent: 08 November 2012 12:49 To: bioconductor at r-project.org; a.beggs at bham.ac.uk Cc: charm Maintainer Subject: CHARM - plotDMRs Hello I was wondering if anyone can help. I have a 4 group exposure for my methylation array experiments, groups one, two, three and four I have used: plotDMRs(dmrs=thedmrs, Genome=Hsapiens, cpg.islands=cpg.cur, exposure=pd$tissue,outfile="./group1-group2.pdf", which_plot=c(1),which_points=c("group1","group2"), smoo="loess", ADD=3000,cols=c("black","red","blue")) To try and plot Group 1 against group 2. However I get: Error: length(cols) >= length(unique(exposure)) is not TRUE I am using the following to generate the DMRs, and finds 125 DMRs: thedmrs = dmrFind(p=p, mod=mod, mod0=mod0, coeff=2, pns=pns, chr=chr, pos=pos) And the output I get is: Running SVA Number of significant surrogate variables is: 10 Iteration (out of 5 ):1 2 3 4 5 Regression Obtaining estimates for factor(pd$tissue, levels = c("group1", "group2", "group3", "group4"))group2 Smoothing == ====================================================================== ======== ................................................... Covariate recognized as categorical. Found 125 potential DMRs Can anyone help? -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] corpcor_1.6.4 BSgenome.Hsapiens.UCSC.hg18_1.3.19 [3] BSgenome_1.26.1 Biostrings_2.26.2 [5] GenomicRanges_1.10.3 IRanges_1.16.4 [7] pd.2006.11.02.hg18.cpg.promo_0.0.1 oligo_1.22.0 [9] oligoClasses_1.20.0 RSQLite_0.11.2 [11] DBI_0.2-5 charm_2.4.0 [13] genefilter_1.40.0 RColorBrewer_1.0-5 [15] fields_6.7 spam_0.29-2 [17] SQN_1.0.5 nor1mix_1.1-3 [19] mclust_4.0 Biobase_2.18.0 [21] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.30.0 affyio_1.26.0 annotate_1.36.0 [4] AnnotationDbi_1.20.2 BiocInstaller_1.8.3 bit_1.1-9 [7] codetools_0.2-8 ff_2.2-9 foreach_1.4.0 [10] gtools_2.7.0 iterators_1.0.6 limma_3.14.1 [13] MASS_7.3-22 multtest_2.14.0 parallel_2.15.2 [16] preprocessCore_1.20.0 siggenes_1.32.0 splines_2.15.2 [19] stats4_2.15.2 survival_2.36-14 sva_3.4.0 [22] tools_2.15.2 XML_3.95-0.1 xtable_1.7-0 [25] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.