DMRcate results meanpvals
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@giovanni-calice-6415
Last seen 9 months ago
Italy

Hi all,

in my DMRcate results concerning two analyses I've very small meanpvals.

In the first analysis the smallest meanpval is 2.65e-210 with cutoff of 7.18e-21;

in the second one the smallest meanpval is 9.19e-305 with cutoff of 1.19e-12 and there are about 40 DMRs with meanpval exactly 0.

The PCA plot shows clearly differences between the groups but I was wondering if something bias the method in my analyses, since there are such small values.

 

Thanks in advance, Regards

 

Giovanni
dmrcate • 2.7k views
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Tim Peters ▴ 200
@tim-peters-7579
Last seen 1 day ago
Australia

Hi Giovanni,

 

I've now run into this error too :)

Fortunately it looks like this line of code is obsolete anyway from running DMR.plot() without it, so I've removed it. Still not sure exactly what the nature of the bug was - GenomicRanges and/or Gviz may have been tweaked recently.

 

Git and svn have been updated - DMRcate_1.8.6 should propagate to Bioconductor in 48 hours. If you can't wait that long please download from the git https://github.com/timpeters82/DMRcate-devel.

 

Many thanks for the bugspot.

Tim
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Hi Tim,

I noticed that this line not influences DMR.plot() running so I've also removed it in my wrapper code.

Thanks, Cheers

Giovanni

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Tim Peters ▴ 200
@tim-peters-7579
Last seen 1 day ago
Australia

Hi Giovanni,

 

meanpval has been deprecated in DMRcate for the last 6 months or so. The Stouffer transformation in more recent versions is a much better indication of the "strength" of the DMR. Please upgrade to the most recent version.

 

Cheers,

Tim
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Hi Tim,

my actual configuration is: R version 3.2.2, Bioconductor version 3.2.

Upgrading DMRcate, It goes to version 1.6.53 and I found the Stouffer transformation is supported.

I try with this version.

 

Thanks, Cheers

Giovanni

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Hi Tim,

the DMRcate version 1.6.53 works fine and I've Stouffer transformation in results.

Only I still have small values of minfdr such as 6.87e-296 but I think already so much better with reasonable value of Stouffer.

 

Thanks again,

Giovanni

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Sorry Tim,

some DMR plots doesn't work, it would appear for DMRs with more overlapping promoters.

This is the error message:

Error in seqnames(methRatios[dmr]) :
  error in evaluating the argument 'x' in selecting a method for function 'seqnames': Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript contains NAs or out-of-bounds indices

What's the matter?

 

Thanks,

Giovanni

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Hi Giovanni,

Since you haven't posted your call to DMR.plot() or sessionInfo() I can only guess as to what the problem is. It may be a bug I've overlooked; it's possible you may have specified the wrong genome and some of your DMRs are outside the natural range of that chromosome, but that's just a guess. I'll need to at least see your call to DMR.plot() and perhaps the head() of the arguments you passed to it to get a feel for the issue. It would be good if you could play around and do some boundary test cases for when it does and doesn't work.

Best,

Tim

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Hi Tim,

the genome is right and this is one call:

DMR.plot(ranges.g2vsg1, dmr = 1, CpGs = Beta.g2vsg1, phen.col = cols.g2vsg1, genome = "hg19")

It works.

ranges.g2vsg1[1]
GRanges object with 1 range and 6 metadata columns:
                        seqnames             ranges strand |   no.cpgs        minfdr                 Stouffer  maxbetafc meanbetafc
                           <Rle>          <IRanges>  <Rle> | <integer>     <numeric>                <numeric>  <numeric>  <numeric>
  chr19:2250561-2253854    chr19 [2250561, 2253854]      * |        18 6.867062e-296 0.0000000000000001105881 -0.6159014 -0.4480837
                                                             overlapping.promoters
                                                                       <character>
  chr19:2250561-2253854 AMH-001, JSRP1-004, AMH-003, MIR4321-201, AMH-002, AMH-004
  -------
  seqinfo: 22 sequences from an unspecified genome; no seqlengths

...

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...

Plots shows exactly the ranges and the promoters associated to dmr1

...

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It doesn't work with dmr = 120 in the call and these are the ranges associated with it:

ranges.g2vsg1[120]
GRanges object with 1 range and 6 metadata columns:
                         seqnames               ranges strand |   no.cpgs                                    minfdr     Stouffer  maxbetafc
                            <Rle>            <IRanges>  <Rle> | <integer>                                 <numeric>    <numeric>  <numeric>
  chr2:45164495-45165527     chr2 [45164495, 45165527]      * |         7 0.000000000000000000000000000000008070301 0.0009529233 -0.5052989
                         meanbetafc                                                  overlapping.promoters
                          <numeric>                                                            <character>
  chr2:45164495-45165527 -0.2788503 RP11-89K21.1-004, RP11-89K21.1-005, RP11-89K21.1-001, RP11-89K21.1-003
  -------
  seqinfo: 22 sequences from an unspecified genome; no seqlengths
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This is the

sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8        LC_COLLATE=it_IT.UTF-8     LC_MONETARY=it_IT.UTF-8   
 [6] LC_MESSAGES=it_IT.UTF-8    LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 doParallel_1.0.10                                 
 [3] lumi_2.22.1                                        DMRcate_1.6.53                                    
 [5] DMRcatedata_1.6.1                                  DSS_2.10.0                                        
 [7] bsseq_1.6.0                                        minfi_1.16.0                                      
 [9] bumphunter_1.10.0                                  locfit_1.5-9.1                                    
[11] iterators_1.0.8                                    foreach_1.4.3                                     
[13] Biostrings_2.38.3                                  XVector_0.10.0                                    
[15] SummarizedExperiment_1.0.2                         GenomicRanges_1.22.3                              
[17] GenomeInfoDb_1.6.1                                 IRanges_2.4.6                                     
[19] S4Vectors_0.8.7                                    lattice_0.20-33                                   
[21] Biobase_2.30.0                                     BiocGenerics_0.16.1                               

loaded via a namespace (and not attached):
 [1] nlme_3.1-122             bitops_1.0-6             matrixStats_0.50.1       RColorBrewer_1.1-2       tools_3.2.2             
 [6] doRNG_1.6                nor1mix_1.2-1            affyio_1.40.0            KernSmooth_2.23-15       rpart_4.1-10            
[11] mgcv_1.8-10              Hmisc_3.17-1             DBI_0.3.1                Gviz_1.14.2              colorspace_1.2-6        
[16] methylumi_2.16.0         nnet_7.3-11              gridExtra_2.0.0          base64_1.1               preprocessCore_1.32.0   
[21] chron_2.3-47             pkgmaker_0.22            rtracklayer_1.30.1       scales_0.3.0             affy_1.48.0             
[26] genefilter_1.52.0        quadprog_1.5-5           stringr_1.0.0            digest_0.6.9             Rsamtools_1.22.0        
[31] foreign_0.8-66           illuminaio_0.12.0        siggenes_1.44.0          R.utils_2.2.0            GEOquery_2.36.0         
[36] dichromat_2.0-0          BSgenome_1.38.0          limma_3.26.5             RSQLite_1.0.0            BiocInstaller_1.20.3    
[41] mclust_5.1               BiocParallel_1.4.3       gtools_3.5.0             acepack_1.3-3.3          R.oo_1.19.0             
[46] VariantAnnotation_1.16.4 RCurl_1.95-4.7           magrittr_1.5             Formula_1.2-1            Matrix_1.2-3            
[51] futile.logger_1.4.1      Rcpp_0.12.3              munsell_0.4.2            R.methodsS3_1.7.0        stringi_1.0-1           
[56] nleqslv_2.9.1            MASS_7.3-45              zlibbioc_1.16.0          plyr_1.8.3               grid_3.2.2              
[61] multtest_2.26.0          GenomicFeatures_1.22.8   annotate_1.48.0          beanplot_1.2             igraph_1.0.1            
[66] rngtools_1.2.4           corpcor_1.6.8            codetools_0.2-14         biomaRt_2.26.1           mixOmics_5.2.0          
[71] futile.options_1.0.0     XML_3.98-1.3             biovizBase_1.18.0        latticeExtra_0.6-26      lambda.r_1.1.7          
[76] data.table_1.9.6         gtable_0.1.2             reshape_0.8.5            ggplot2_2.0.0            xtable_1.8-0            
[81] survival_2.38-3          GenomicAlignments_1.6.3  AnnotationDbi_1.32.3     registry_0.3             ellipse_0.3-8           
[86] cluster_2.0.3            rgl_0.95.1441

I do not know if I have to post something else.

Best,

Giovanni

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Debugging code I notice that just this line

extras <- endoapply(extras, function(x) {    
        chromosome(x) <- as.character(seqnames(methRatios[dmr]))
        x
    })

gives sometimes error.

Hope that this helps,
Giovanni

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Hi Giovanni,

From memory there was still a bit of an issue with DMR.plot() in 1.6.53 / R 3.2.2. Please upgrade to DMRcate_1.8.5 / R_3.3.0 and run your analysis again.

If you're still getting the same error, have a look at the values of

as.character(seqnames(methRatios[dmr]))

when you're debugging and see if you can figure out if and why they are different to those that work.

If that fails, send me your R code and workspace objects in a dropbox link and I'll figure out what's going wrong. 

Cheers,

Tim

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Hi Tim,

I upgrade everything but I'm still getting the same error.

In the case it works the value is the chromosome number (for dmr1 as I posted data earlier in the thread, the value is chr19).

In the case It fails, you can not see the value and the run stops with the same error:

Error: subscript contains NAs or out-of-bounds indices

...

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This is the new

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8        LC_COLLATE=it_IT.UTF-8    
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=it_IT.UTF-8    LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 doParallel_1.0.10                                 
 [3] lumi_2.24.0                                        DMRcate_1.8.5                                     
 [5] DMRcatedata_1.8.2                                  DSS_2.12.0                                        
 [7] bsseq_1.8.2                                        limma_3.28.14                                     
 [9] minfi_1.18.2                                       bumphunter_1.12.0                                 
[11] locfit_1.5-9.1                                     iterators_1.0.8                                   
[13] foreach_1.4.3                                      Biostrings_2.40.2                                 
[15] XVector_0.12.0                                     SummarizedExperiment_1.2.3                        
[17] GenomicRanges_1.24.2                               GenomeInfoDb_1.8.1                                
[19] IRanges_2.6.1                                      S4Vectors_0.10.1                                  
[21] lattice_0.20-33                                    Biobase_2.32.0                                    
[23] BiocGenerics_0.18.0                                BiocInstaller_1.22.3                              

loaded via a namespace (and not attached):
 [1] nlme_3.1-128                  bitops_1.0-6                  matrixStats_0.50.2            RColorBrewer_1.1-2           
 [5] httr_1.2.0                    tools_3.3.1                   doRNG_1.6                     nor1mix_1.2-1                
 [9] affyio_1.42.0                 R6_2.1.2                      KernSmooth_2.23-15            rpart_4.1-10                 
[13] mgcv_1.8-12                   Hmisc_3.17-4                  DBI_0.4-1                     Gviz_1.16.1                  
[17] colorspace_1.2-6              methylumi_2.18.2              permute_0.9-0                 nnet_7.3-12                  
[21] gridExtra_2.2.1               base64_2.0                    preprocessCore_1.34.0         chron_2.3-47                 
[25] pkgmaker_0.22                 rtracklayer_1.32.1            scales_0.4.0                  affy_1.50.0                  
[29] genefilter_1.54.2             quadprog_1.5-5                stringr_1.0.0                 digest_0.6.9                 
[33] Rsamtools_1.24.0              foreign_0.8-66                illuminaio_0.14.0             siggenes_1.46.0              
[37] R.utils_2.3.0                 GEOquery_2.38.4               htmltools_0.3.5               dichromat_2.0-0              
[41] BSgenome_1.40.1               ensembldb_1.4.6               RSQLite_1.0.0                 shiny_0.13.2                 
[45] mclust_5.2                    BiocParallel_1.6.2            gtools_3.5.0                  acepack_1.3-3.3              
[49] R.oo_1.20.0                   VariantAnnotation_1.18.1      RCurl_1.95-4.8                magrittr_1.5                 
[53] Formula_1.2-1                 Matrix_1.2-6                  Rcpp_0.12.5                   munsell_0.4.3                
[57] R.methodsS3_1.7.1             stringi_1.1.1                 nleqslv_3.0.2                 MASS_7.3-45                  
[61] zlibbioc_1.18.0               plyr_1.8.4                    AnnotationHub_2.4.2           grid_3.3.1                   
[65] multtest_2.28.0               GenomicFeatures_1.24.3        annotate_1.50.0               beanplot_1.2                 
[69] rngtools_1.2.4                codetools_0.2-14              biomaRt_2.28.0                XML_3.98-1.4                 
[73] biovizBase_1.20.0             latticeExtra_0.6-28           data.table_1.9.6              httpuv_1.3.3                 
[77] gtable_0.2.0                  openssl_0.9.4                 reshape_0.8.5                 ggplot2_2.1.0                
[81] mime_0.4                      xtable_1.8-2                  survival_2.39-5               GenomicAlignments_1.8.3      
[85] AnnotationDbi_1.34.3          registry_0.3                  cluster_2.0.4                 interactiveDisplayBase_1.10.3

Cheers,

Giovanni

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