Question: Champ.lasso error @ dmr.beta.means[,22:24]
gravatar for zhourudy2
4.3 years ago by
zhourudy210 wrote:

Package source v1.6.0

trace: champ.lasso(fromFile = T, limma = annottated, beta.norm = batchNorm$beta, 
    batchDone = TRUE, pd = myLoad$pd, image = F, bedFile = FALSE, 
    resultsDir = getwd())
Run Probe Lasso DMR Hunter
Error in `[.data.frame`(dmr.beta.means, , 22:24, ) : 
  undefined columns selected


Using default champ.lasso and limma returns this error, was able to remedy by changing column reference to [,17:19]. Can only guess it is referring to the wrong columns in the limma results obtained from champ.MVP




> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages:
 [1] IlluminaHumanMethylation450kmanifest_0.4.0         ChAMP_1.6.0                                        Illumina450ProbeVariants.db_1.4.0                 
 [4] ChAMPdata_1.6.0                                    wateRmelon_1.8.0                                   IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [7] ROC_1.44.0                                         lumi_2.20.2                                        methylumi_2.14.0                                  
[10] minfi_1.14.0                                       bumphunter_1.8.0                                   locfit_1.5-9.1                                    
[13] iterators_1.0.7                                    foreach_1.4.2                                      Biostrings_2.36.1                                 
[16] XVector_0.8.0                                      lattice_0.20-31                                    FDb.InfiniumMethylation.hg19_2.2.0                
[19]                                 RSQLite_1.0.0                                      DBI_0.3.1                                         
[22] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2            GenomicFeatures_1.20.1                             AnnotationDbi_1.30.1                              
[25] GenomicRanges_1.20.5                               GenomeInfoDb_1.4.1                                 IRanges_2.2.5                                     
[28] S4Vectors_0.6.1                                    ggplot2_1.0.1                                      reshape2_1.4.1                                    
[31] scales_0.2.5                                       Biobase_2.28.0                                     BiocGenerics_0.14.0                               
[34] matrixStats_0.14.2                                 limma_3.24.13                                      plyr_1.8.3                                        

loaded via a namespace (and not attached):
 [1] nlme_3.1-121            bitops_1.0-6            RColorBrewer_1.1-2      tools_3.2.1             doRNG_1.6               nor1mix_1.2-0          
 [7] affyio_1.36.0           KernSmooth_2.23-15      mgcv_1.8-6              colorspace_1.2-6        DNAcopy_1.42.0          base64_1.1             
[13] preprocessCore_1.30.0   RPMM_1.20               pkgmaker_0.22           rtracklayer_1.28.6      genefilter_1.50.0       quadprog_1.5-5         
[19] affy_1.46.1             stringr_1.0.0           digest_0.6.8            Rsamtools_1.20.4        illuminaio_0.10.0       siggenes_1.42.0        
[25] GEOquery_2.34.0         impute_1.42.0           BiocInstaller_1.18.3    mclust_5.0.2            BiocParallel_1.2.8      RCurl_1.95-4.7         
[31] magrittr_1.5            futile.logger_1.4.1     Matrix_1.2-2            Rcpp_0.11.6             munsell_0.4.2           proto_0.3-10           
[37] stringi_0.5-5           nleqslv_2.8             MASS_7.3-42             zlibbioc_1.14.0         grid_3.2.1              splines_3.2.1          
[43] multtest_2.24.0         annotate_1.46.0         beanplot_1.2            rngtools_1.2.4          marray_1.46.0           codetools_0.2-11       
[49] biomaRt_2.24.0          futile.options_1.0.0    XML_3.98-1.3            lambda.r_1.1.7          gtable_0.1.2            reshape_0.8.5          
[55] xtable_1.7-4            survival_2.38-3         GenomicAlignments_1.4.1 registry_0.3            cluster_2.0.2           sva_3.14.0  

champ • 705 views
ADD COMMENTlink modified 3.8 years ago by david.watson10 • written 4.3 years ago by zhourudy210
Answer: Champ.lasso error @ dmr.beta.means[,22:24]
gravatar for yourell.alan
4.2 years ago by
United Kingdom
yourell.alan10 wrote:

Hi Rudy,

I have got the same error except I am not using the output from champ.MVP. Instead I am using the output from Limma topTable. Any ideas on what might be happening? I assume it is searching for a column that doesn't exist in data. Am I even using the right data?


Any help much appreciated,


ADD COMMENTlink written 4.2 years ago by yourell.alan10
Answer: Champ.lasso error @ dmr.beta.means[,22:24]
gravatar for david.watson
3.8 years ago by
Queen Mary University of London
david.watson10 wrote:

There's an extra comma in the source code for champ.lasso at line 211 defining dmr.beta.means. You can tell from the error message, where there are commas before and after the column specification. Try deleting the second comma and rerunning. 




ADD COMMENTlink written 3.8 years ago by david.watson10
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