Question: affycoretools::annotateEset unable to find inherited method
0
gravatar for willie.yu.ncc
17 months ago by
Singapore/Duke-NUS Medical School
willie.yu.ncc0 wrote:

When I tried to use the annotateEset function in affycoretools, it complains and output the following message.

>annotateEset()
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'annotateEset' for signature '"missing", "missing"'


I re-installed the affycoretools package and it appears the annotateEset function is just a holder ...

annotateEset                            html  
Rd warning: /tmp/RtmpE53Lt8/R.INSTALL40a34bd7bc8a/affycoretools/man/annotateEset.Rd:47: file link 'columns' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpE53Lt8/R.INSTALL40a34bd7bc8a/affycoretools/man/annotateEset.Rd:50: file link 'mapIds' in package 'AnnotationDbi' does not exist and so has been treated as a topic


So it complains about not finding columns and mapIds functions from AnnotationDbi package so re-installed that and checked for existence of the missing two functions below.

> columns
nonstandardGenericFunction for "columns" defined from package "AnnotationDbi"

function (x)
{
    value <- standardGeneric("columns")
    sort(value)
}
<bytecode: 0x563dec99a368>
<environment: 0x563dec9ae258>
Methods may be defined for arguments: x
Use  showMethods("columns")  for currently available ones.
> mapIds
standardGeneric for "mapIds" defined from package "AnnotationDbi"

function (x, keys, column, keytype, ..., multiVals)
standardGeneric("mapIds")
<bytecode: 0x563df0aa2398>
<environment: 0x563df0a9b790>
Methods may be defined for arguments: x
Use  showMethods("mapIds")  for currently available ones.


So both functions exists in AnnotationDbi so I don't know why affycoretools is not able to locate them =/.

 

Below is my session info if that helps with the diagnostics.

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 27 (Twenty Seven)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

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

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

other attached packages:
[1] affycoretools_1.52.1 AnnotationDbi_1.42.1 IRanges_2.14.10     
[4] S4Vectors_0.18.3     Biobase_2.40.0       BiocGenerics_0.26.0
[7] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2            hwriter_1.3.2              
  [3] biovizBase_1.28.0           htmlTable_1.12             
  [5] XVector_0.20.0              GenomicRanges_1.32.3       
  [7] base64enc_0.1-3             dichromat_2.0-0            
  [9] rstudioapi_0.7              affyio_1.50.0              
 [11] bit64_0.9-7                 codetools_0.2-15           
 [13] oligoClasses_1.42.0         splines_3.5.0              
 [15] R.methodsS3_1.7.1           ggbio_1.28.0               
 [17] geneplotter_1.58.0          knitr_1.20                 
 [19] Formula_1.2-3               Rsamtools_1.32.0           
 [21] annotate_1.58.0             cluster_2.0.7-1            
 [23] GO.db_3.6.0                 R.oo_1.22.0                
 [25] graph_1.58.0                compiler_3.5.0             
 [27] httr_1.3.1                  GOstats_2.46.0             
 [29] backports_1.1.2             assertthat_0.2.0           
 [31] Matrix_1.2-14               lazyeval_0.2.1             
 [33] limma_3.36.2                acepack_1.4.1              
 [35] htmltools_0.3.6             prettyunits_1.0.2          
 [37] tools_3.5.0                 gtable_0.2.0               
 [39] GenomeInfoDbData_1.1.0      affy_1.58.0                
 [41] Category_2.46.0             reshape2_1.4.3             
 [43] Rcpp_0.12.17                Biostrings_2.48.0          
 [45] gdata_2.18.0                preprocessCore_1.42.0      
 [47] rtracklayer_1.40.3          iterators_1.0.9            
 [49] stringr_1.3.1               ensembldb_2.4.1            
 [51] gtools_3.5.0                XML_3.98-1.11              
 [53] edgeR_3.22.3                zlibbioc_1.26.0            
 [55] scales_0.5.0                BSgenome_1.48.0            
 [57] VariantAnnotation_1.26.0    hms_0.4.2                  
 [59] ProtGenerics_1.12.0         SummarizedExperiment_1.10.1
 [61] RBGL_1.56.0                 AnnotationFilter_1.4.0     
 [63] RColorBrewer_1.1-2          curl_3.2                   
 [65] memoise_1.1.0               gridExtra_2.3              
 [67] ggplot2_2.2.1               biomaRt_2.36.1             
 [69] rpart_4.1-13                gcrma_2.52.0               
 [71] reshape_0.8.7               latticeExtra_0.6-28        
 [73] stringi_1.2.3               RSQLite_2.1.1              
 [75] genefilter_1.62.0           foreach_1.4.4              
 [77] checkmate_1.8.5             caTools_1.17.1             
 [79] GenomicFeatures_1.32.0      BiocParallel_1.14.1        
 [81] GenomeInfoDb_1.16.0         ReportingTools_2.20.0      
 [83] rlang_0.2.1                 pkgconfig_2.0.1            
 [85] matrixStats_0.53.1          bitops_1.0-6               
 [87] lattice_0.20-35             GenomicAlignments_1.16.0   
 [89] htmlwidgets_1.2             bit_1.1-14                 
 [91] GSEABase_1.42.0             AnnotationForge_1.22.0     
 [93] GGally_1.4.0                plyr_1.8.4                 
 [95] magrittr_1.5                DESeq2_1.20.0              
 [97] R6_2.2.2                    gplots_3.0.1               
 [99] Hmisc_4.1-1                 DelayedArray_0.6.1         
[101] DBI_1.0.0                   pillar_1.2.3               
[103] foreign_0.8-70              survival_2.42-3            
[105] RCurl_1.95-4.10             nnet_7.3-12                
[107] tibble_1.4.2                crayon_1.3.4               
[109] KernSmooth_2.23-15          OrganismDbi_1.22.0         
[111] PFAM.db_3.6.0               progress_1.2.0             
[113] locfit_1.5-9.1              grid_3.5.0                 
[115] data.table_1.11.4           blob_1.1.1                 
[117] Rgraphviz_2.24.0            digest_0.6.15              
[119] xtable_1.8-2                ff_2.2-14                  
[121] R.utils_2.6.0               munsell_0.5.0              
[123] tcltk_3.5.0 
ADD COMMENTlink modified 17 months ago by James W. MacDonald51k • written 17 months ago by willie.yu.ncc0
Answer: affycoretools::annotateEset unable to find inherited method
0
gravatar for James W. MacDonald
17 months ago by
United States
James W. MacDonald51k wrote:

If you try to run a function that has required arguments, but you don't supply any arguments, you should not be surprised that things don't work correctly. What did you think

annotateEset()

Would do? If you don't give it an ExpressionSet to annotate, nor an annotation package to use, I am not sure what the expectation should be.

Also, you are misdiagnosing the warnings you see when installing. Those have to do with the help pages, and won't have any effect on the function at all.

ADD COMMENTlink written 17 months ago by James W. MacDonald51k

I see then I am not sure how to explain the following when I ran the annotateEset command for my data set ....

> library("affycoretools", lib.loc="~/R/x86_64-redhat-linux-gnu-library/3.5")

> library("clariomsmousetranscriptcluster.db", lib.loc="~/R/x86_64-redhat-linux-gnu-library/3.5")

> head( CEL_filterData )
ExpressionFeatureSet (storageMode: lockedEnvironment)
assayData: 1 features, 97 samples
  element names: exprs
protocolData
  rowNames: AH107 AH112 ... AH9 (97 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: AH107 AH112 ... AH9 (97 total)
  varLabels: index GENOTYPE ... INJECTION_TIME (5 total)
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.clariom.s.mouse

Everything looks good then this happens ...

> annotateEset( CEL_filterData, clariomsmousetranscriptcluster.db )
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'annotateEset' for signature '"ExpressionFeatureSet", "ChipDb"'

My session info is below:

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 27 (Twenty Seven)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

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

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

other attached packages:
 [1] BiocInstaller_1.30.0                    pd.clariom.s.mouse_3.14.1               DBI_1.0.0                              
 [4] oligo_1.44.0                            RSQLite_2.1.1                           Biostrings_2.48.0                      
 [7] XVector_0.20.0                          clariomsmousetranscriptcluster.db_8.7.0 org.Mm.eg.db_3.6.0                     
[10] AnnotationDbi_1.42.1                    IRanges_2.14.10                         S4Vectors_0.18.3                       
[13] affycoretools_1.52.1                    Biobase_2.40.0                          BiocGenerics_0.26.0                    
[16] oligoClasses_1.42.0                    

 

 

ADD REPLYlink modified 17 months ago • written 17 months ago by willie.yu.ncc0

You cannot annotate an ExpressionFeatureSet, as that contains data prior to summarization. You need to run rma first.

ADD REPLYlink written 16 months ago by James W. MacDonald51k
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