Deleted:When trying to Annotate affimetrix microarray an empty data.frame is retrieved
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ANDY • 0
@4f3cf502
Last seen 2.3 years ago
United States

Hi, I'm just working in a simple use case of the biomaRt package to annotate Affimetrix, using the hg version seen in the console etc. but for some reason I'm not being able to retrieve data corresponding to chip affy_hg_u95av2, Thank you in advance, for any contribution to resolving this issue.

Code should be placed in three backticks as shown below


library(biomaRt)

# Package ALL - EXPERIMENTAL DATA PACKAGE of BIOCONDUCTOR
BiocManager::install("ALL")
library(ALL)
ALL
# ExpressionSet (storageMode: lockedEnvironment)
# assayData: 12625 features, 128 samples  <<--------------SEE THE AMOUNT OF FEATURES
# element names: exprs 
# protocolData: none
# phenoData
# sampleNames: 01005 01010 ... LAL4 (128 total)
# varLabels: cod diagnosis ... date last seen (21 total)

# LOAD EXPERIMENTAL DATA PACKAGE
data(ALL)
ALL

# GET A MART
mart <- useMart(host="feb2014.archive.ensembl.org", biomart = "ENSEMBL_MART_ENSEMBL")
mart

# GET A DATASSET:
listDatasets(mart)
# 80           hsapiens_gene_ensembl                                     Human genes (GRCh38.p14)
ensemblDataSet <- useDataset("hsapiens_gene_ensembl", mart)

# ANNOTATE:Now we going to annotate the dataset:
# FIRST get these features we want to annotate using Biobase::featureNames():
# ALL:: get some ID's
ALLFeaturesNames = Biobase::featureNames(ALL)#[1:12625]
ALLFeaturesNames

# CHIPS NAMES (notice that these are NOT the called affymetrix probes IDs )
affy.chips$name[grep("*_at",affy.chips$description)]
# [1] "affy_hc_g110"            "affy_hg_focus"           "affy_hg_u133a_2"        
# [4] "affy_hg_u133b"           "affy_hg_u133_plus_2"     "affy_hg_u95a"           
# [7] "affy_hg_u95av2"          "affy_hg_u95b"            "affy_hg_u95c"           
# [10] "affy_hg_u95d"            "affy_hg_u95e"            "affy_ht_hg_u133_plus_pm"
# [13] "affy_hugenefl"           "affy_primeview"          "affy_u133_x3p"

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 


# FINALLY ANNOTATE:
ALLFeaturesNamesAnotated <- 
getBM(attributes = c("ensembl_gene_id","affy_hg_u95av2"), 
          filters="affy_hg_u95av2", 
      values = "values", mart = ensembl)  


# But here Im getting just an empty data.frame 
[1] ensembl_gene_id affy_hg_u95av2 
<0 rows> (or 0-length row.names)



#=====================================================================================
#=====================================================================================
sessionInfo( )

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

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

other attached packages: [1] devtools_2.4.5 usethis_2.2.2 airway_1.18.0
[4] hgu95av2.db_3.13.0 org.Hs.eg.db_3.16.0 AnnotationDbi_1.60.2
[7] ALL_1.40.0 biomaRt_2.54.1 GEOquery_2.66.0
[10] BSgenome_1.66.3 Biostrings_2.66.0 XVector_0.38.0
[13] rtracklayer_1.58.0 SummarizedExperiment_1.28.0 Biobase_2.58.0
[16] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 MatrixGenerics_1.10.0
[19] matrixStats_0.63.0 AnnotationHub_3.6.0 BiocFileCache_2.6.1
[22] dbplyr_2.3.2 IRanges_2.32.0 S4Vectors_0.36.2
[25] BiocGenerics_0.44.0

loaded via a namespace (and not attached): [1] fs_1.6.2 bitops_1.0-7 bit64_4.0.5
[4] filelock_1.0.2 progress_1.2.2 httr_1.4.6
[7] profvis_0.3.8 tools_4.2.2 utf8_1.2.3
[10] R6_2.5.1 DBI_1.1.3 urlchecker_1.0.1
[13] withr_2.5.0 processx_3.8.1 tidyselect_1.2.0
[16] prettyunits_1.1.1 bit_4.0.5 curl_5.0.0
[19] compiler_4.2.2 cli_3.6.1 xml2_1.3.5
[22] DelayedArray_0.24.0 readr_2.1.4 callr_3.7.3
[25] rappdirs_0.3.3 stringr_1.5.0 digest_0.6.31
[28] Rsamtools_2.14.0 R.utils_2.12.2 pkgconfig_2.0.3
[31] htmltools_0.5.5 sessioninfo_1.2.2 fastmap_1.1.1
[34] limma_3.54.2 htmlwidgets_1.6.2 rlang_1.1.1
[37] rstudioapi_0.15.0 RSQLite_2.3.1 shiny_1.7.4.1
[40] BiocIO_1.8.0 generics_0.1.3 BiocParallel_1.32.6
[43] R.oo_1.25.0 dplyr_1.1.2 RCurl_1.98-1.12
[46] magrittr_2.0.3 GenomeInfoDbData_1.2.9 Matrix_1.5-1
[49] Rcpp_1.0.10 fansi_1.0.4 lifecycle_1.0.3
[52] R.methodsS3_1.8.2 stringi_1.7.12 yaml_2.3.7
[55] zlibbioc_1.44.0 pkgbuild_1.4.2 grid_4.2.2
[58] blob_1.2.4 parallel_4.2.2 promises_1.2.0.1
[61] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.20-45
[64] hms_1.1.3 KEGGREST_1.38.0 ps_1.7.5
[67] pillar_1.9.0 rjson_0.2.21 pkgload_1.3.2.1
[70] codetools_0.2-18 XML_3.99-0.14 glue_1.6.2
[73] BiocVersion_3.16.0 remotes_2.4.2.1 data.table_1.14.8
[76] BiocManager_1.30.21.1 png_0.1-8 vctrs_0.6.2
[79] tzdb_0.4.0 httpuv_1.6.11 purrr_1.0.1
[82] tidyr_1.3.0 cachem_1.0.8 mime_0.12
[85] xtable_1.8-4 restfulr_0.0.15 later_1.3.1
[88] tibble_3.2.1 GenomicAlignments_1.34.1 memoise_2.0.1
[91] ellipsis_0.3.2 interactiveDisplayBase_1.36.0

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