[BioC] CHARM - plotDMRs

[Andrew Beggs [guest]]

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 

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