claariom.s.human annotation error
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Entering edit mode
tangming2005 ▴ 170
@tangming2005-6754
Last seen 12 months ago
United States

code are below.

Thank you!

library(limma)
library(oligo)
library(pd.clariom.s.human)

celFiles <- list.celfiles('.', full.names=TRUE)
ab<- read.celfiles(celFiles)

eset<- oligo::rma(ab)

library("affycoretools")

eset <- annotateEset(eset, annotation(eset))

Error: There appears to be a mismatch between the ExpressionSet and the annotation data.
Please ensure that the summarization level for the ExpressionSet and the 'type' argument are the same.
 See ?annotateEset for more information on the type argument.

eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 27189 features, 37 samples 
  element names: exprs 
protocolData
  rowNames: Pa25N1_101817_(Clariom_S_Human).CEL Pa25T1_101817_(Clariom_S_Human).CEL ...
    Pa37T2_101817_(Clariom_S_Human).CEL (37 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: Pa25N1_101817_(Clariom_S_Human).CEL Pa25T1_101817_(Clariom_S_Human).CEL ...
    Pa37T2_101817_(Clariom_S_Human).CEL (37 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.clariom.s.human 


> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] affycoretools_1.48.0                    ggrepel_0.7.0                          
 [3] stringr_1.2.0                           pd.clariom.s.human_3.14.1              
 [5] DBI_0.7                                 oligo_1.40.2                           
 [7] oligoClasses_1.38.0                     RSQLite_2.0                            
 [9] Biostrings_2.44.2                       XVector_0.16.0                         
[11] limma_3.32.10                           ComplexHeatmap_1.14.0                  
[13] bindrcpp_0.2                            rtracklayer_1.36.5                     
[15] dplyr_0.7.4                             purrr_0.2.3                            
[17] readr_1.1.1                             tidyr_0.7.1                            
[19] tibble_1.3.4                            ggplot2_2.2.1                          
[21] tidyverse_1.1.1                         org.Hs.eg.db_3.4.1                     
[23] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.28.5                 
[25] AnnotationDbi_1.38.2                    Biobase_2.36.2                         
[27] GenomicRanges_1.28.6                    GenomeInfoDb_1.12.3                    
[29] IRanges_2.10.5                          S4Vectors_0.14.7                       
[31] BiocGenerics_0.22.1                     here_0.1                               

loaded via a namespace (and not attached):
  [1] R.utils_2.6.0                 htmlwidgets_0.9               trimcluster_0.1-2            
  [4] BiocParallel_1.10.1           munsell_0.4.3                 codetools_0.2-15             
  [7] preprocessCore_1.38.1         colorspace_1.3-2              BiocInstaller_1.26.1         
 [10] OrganismDbi_1.18.1            Category_2.42.1               knitr_1.17                   
 [13] robustbase_0.92-7             labeling_0.3                  GenomeInfoDbData_0.99.0      
 [16] hwriter_1.3.2                 mnormt_1.5-5                  bit64_0.9-7                  
 [19] rprojroot_1.2                 biovizBase_1.24.0             diptest_0.75-7               
 [22] affxparser_1.48.0             R6_2.2.2                      locfit_1.5-9.1               
 [25] AnnotationFilter_1.0.0        flexmix_2.3-14                bitops_1.0-6                 
 [28] reshape_0.8.7                 DelayedArray_0.2.7            assertthat_0.2.0             
 [31] scales_0.5.0                  nnet_7.3-12                   gtable_0.2.0                 
 [34] affy_1.54.0                   ggbio_1.24.1                  ensembldb_2.0.4              
 [37] rlang_0.1.2                   genefilter_1.58.1             GlobalOptions_0.0.12         
 [40] splines_3.4.2                 lazyeval_0.2.0                acepack_1.4.1                
 [43] dichromat_2.0-0               broom_0.4.2                   checkmate_1.8.4              
 [46] yaml_2.1.14                   reshape2_1.4.2                modelr_0.1.1                 
 [49] backports_1.1.1               httpuv_1.3.5                  Hmisc_4.0-3                  
 [52] RBGL_1.52.0                   tools_3.4.2                   psych_1.7.8                  
 [55] gplots_3.0.1                  affyio_1.46.0                 ff_2.2-13                    
 [58] RColorBrewer_1.1-2            Rcpp_0.12.13                  plyr_1.8.4                   
 [61] base64enc_0.1-3               zlibbioc_1.22.0               RCurl_1.95-4.8               
 [64] rpart_4.1-11                  GetoptLong_0.1.6              viridis_0.4.0                
 [67] SummarizedExperiment_1.6.5    haven_1.1.0                   cluster_2.0.6                
 [70] magrittr_1.5                  data.table_1.10.4-3           circlize_0.4.1               
 [73] mvtnorm_1.0-6                 whisker_0.3-2                 ProtGenerics_1.8.0           
 [76] matrixStats_0.52.2            hms_0.3                       mime_0.5                     
 [79] xtable_1.8-2                  XML_3.98-1.9                  gcrma_2.48.0                 
 [82] mclust_5.3                    readxl_1.0.0                  gridExtra_2.3                
 [85] shape_1.4.3                   compiler_3.4.2                biomaRt_2.32.1               
 [88] KernSmooth_2.23-15            R.oo_1.21.0                   ReportingTools_2.16.0        
 [91] htmltools_0.3.6               GOstats_2.42.0                Formula_1.2-2                
 [94] geneplotter_1.54.0            lubridate_1.6.0               MASS_7.3-47                  
 [97] fpc_2.1-10                    Matrix_1.2-11                 gdata_2.18.0                 
[100] R.methodsS3_1.7.1             bindr_0.1                     forcats_0.2.0                
[103] pkgconfig_2.0.1               GenomicAlignments_1.12.2      foreign_0.8-69               
[106] xml2_1.1.1                    foreach_1.4.3                 annotate_1.54.0              
[109] AnnotationForge_1.18.2        rvest_0.3.2                   VariantAnnotation_1.22.3     
[112] digest_0.6.12                 graph_1.54.0                  cellranger_1.1.0             
[115] htmlTable_1.9                 dendextend_1.5.2              edgeR_3.18.1                 
[118] GSEABase_1.38.2               curl_3.0                      kernlab_0.9-25               
[121] gtools_3.5.0                  shiny_1.0.5                   Rsamtools_1.28.0             
[124] modeltools_0.2-21             rjson_0.2.15                  nlme_3.1-131                 
[127] jsonlite_1.5                  PFAM.db_3.4.1                 viridisLite_0.2.0            
[130] BSgenome_1.44.2               lattice_0.20-35               GGally_1.3.2                 
[133] httr_1.3.1                    DEoptimR_1.0-8                survival_2.41-3              
[136] GO.db_3.4.1                   interactiveDisplayBase_1.14.0 glue_1.1.1                   
[139] prabclus_2.2-6                iterators_1.0.8               bit_1.1-12                   
[142] class_7.3-14                  stringi_1.1.5                 blob_1.1.0                   
[145] DESeq2_1.16.1                 AnnotationHub_2.8.3           caTools_1.17.1               
[148] latticeExtra_0.6-28           memoise_1.1.0 
affcoretools pd.clariom.s.human • 1.3k views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 14 hours ago
United States

You have a mixture of packages, some that are current, and some that are up to two releases out of date (affycoretools and oligo to name two). You are liable to get odd errors running a non-standard installation like that, and we don't support people who choose to do so (on the assumption that if you are knowledgeable enough to decide you need a non-standard setup, you are also knowledgeable enough to troubleshoot your own problems).

I can't imagine why you would want to have such a setup, and would recommend doing

library(BiocInstaller)

biocLite()

to correct your installation. That said, there is a problem with affycoretools in this instance, where I am probably using the wrong test to make sure you get the right annotation package. I will fix that in the release version of affycoretools, which you can get in a day or so, using biocLite.

In the meantime, do note that you really don't need to annotate that way. You could instead do:

library(clariomshumantranscriptcluster.db)

eset <- annotateEset(eset, clariomshumantranscriptcluster.db)

which will work.

ADD COMMENT
0
Entering edit mode

Thanks James. I upgraded R to the current. and somehow the old bioc packages are still linked to the new R version...

The other way indeed worked.

Best,

Ming

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