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Question: conumee error: query intensities not given for all probes.
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gravatar for yura.grabovska
5 weeks ago by
yura.grabovska0 wrote:
Conumee error:

Error in .local(query, ref, anno, ...) : 
  query intensities not given for all probes.

 

This error results when I use 

x <- CNV.fit(data[1], controls.data, anno)

The data object was generated by:

rgSet <- combineArrays(rgSet.450k, rgSet.850k)
mSet <- preprocessNoob(rgSet, dyeMethod = "single")
data <- CNV.load(mSet)

 

The anno object was made by: 

anno <- CNV.create_anno(chrXY = TRUE, 
                        exclude_regions = exclude_regions, 
                        detail_regions = detail_regions,
                        array_type = "overlap")

Controls data is generated in a similar way to the test data.

Could you please let me what checks to carry out? I current work around this by amending the anno data to reflect the missing problems and end up dropping quite a number of probes in the process. 

Many thanks

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
 [1] conumee_1.10.0                                      IlluminaHumanMethylationEPICmanifest_0.3.0          IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
 [4] IlluminaHumanMethylation450kmanifest_0.4.0          IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0  minfi_1.22.1                                       
 [7] bumphunter_1.16.0                                   locfit_1.5-9.1                                      iterators_1.0.8                                    
[10] foreach_1.4.3                                       Biostrings_2.44.1                                   XVector_0.16.0                                     
[13] SummarizedExperiment_1.6.3                          DelayedArray_0.2.7                                  matrixStats_0.52.2                                 
[16] Biobase_2.36.2                                      GenomicRanges_1.28.3                                GenomeInfoDb_1.12.2                                
[19] IRanges_2.10.2                                      S4Vectors_0.14.3                                    BiocGenerics_0.22.0                                

loaded via a namespace (and not attached):
 [1] httr_1.2.1               nor1mix_1.2-2            bit64_0.9-7              splines_3.4.0            doRNG_1.6.6              blob_1.1.0              
 [7] GenomeInfoDbData_0.99.0  Rsamtools_1.28.0         RSQLite_2.0              lattice_0.20-35          limma_3.32.2             quadprog_1.5-5          
[13] digest_0.6.12            RColorBrewer_1.1-2       preprocessCore_1.38.1    Matrix_1.2-10            plyr_1.8.4               GEOquery_2.42.0         
[19] siggenes_1.50.0          XML_3.98-1.9             biomaRt_2.32.1           genefilter_1.58.1        zlibbioc_1.22.0          xtable_1.8-2            
[25] BiocParallel_1.10.1      tibble_1.3.3             openssl_0.9.6            annotate_1.54.0          beanplot_1.2             pkgmaker_0.22           
[31] GenomicFeatures_1.28.4   survival_2.41-3          magrittr_1.5             mclust_5.3               memoise_1.1.0            nlme_3.1-131            
[37] MASS_7.3-47              tools_3.4.0              registry_0.3             data.table_1.10.4        stringr_1.2.0            rngtools_1.2.4          
[43] AnnotationDbi_1.38.1     base64_2.0               compiler_3.4.0           rlang_0.1.1              grid_3.4.0               RCurl_1.95-4.8          
[49] bitops_1.0-6             DNAcopy_1.50.1           codetools_0.2-15         multtest_2.32.0          DBI_0.7                  reshape_0.8.6           
[55] R6_2.2.2                 illuminaio_0.18.0        GenomicAlignments_1.12.1 rtracklayer_1.36.3       bit_1.1-12               stringi_1.1.5           
[61] Rcpp_0.12.11            
 
 

 

 

ADD COMMENTlink modified 6 days ago by SplittingInfinity0 • written 5 weeks ago by yura.grabovska0
2
gravatar for volker hovestadt
5 weeks ago by
boston
volker hovestadt20 wrote:

there are some probes missing on more recent EPIC arrays which causes this error.

for now you can try installing the more recent "IlluminaHumanMethylationEPICanno.ilm10b3.hg19" package and adapt the "CNV.create_anno" function (line 96: https://github.com/Bioconductor-mirror/conumee/blob/release-3.5/R/annotation.R).

i will fix this in the next release. thank you for reporting this bug.

 

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by volker hovestadt20

Thank you for getting back to me. We assumed there was something going on along these lines as I recently had a similar problem with minfi reading in newer EPIC array idats before the update dropped. 

Will implement change you recommended.

ADD REPLYlink written 5 weeks ago by yura.grabovska0
0
gravatar for SplittingInfinity
6 days ago by
SplittingInfinity0 wrote:

I had the same problem as well. In case this may be interesting to others, the temporary measure that I'm doing is finding the overlaps between sample and anno file right after CNV.load:

data <- CNV.load(Mset)

controls.data <- CNV.load(MsetControls)

### find overlaps ###

Mset <- mapToGenome(Mset)

anno@probes <- subsetByOverlaps(anno@probes, granges(Mset))
ADD COMMENTlink written 6 days ago by SplittingInfinity0
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