Gene expression annotation for microarray from BiomaRt R package

Question

[Sara]

Hi, I am in need of an updated version of annotation file for gene expression from BiomaRt R package in an R readable format. I would like to have the cleaned annotation file meaning to have probes, genes, other information, such as genomic coordinates,.... Any one can help with this? thanks.

[Matthias Zepper]

Unless somebody here happens to be a clairvoyant, you should at least specify the platform you are looking for. Also, pre-downloaded annotation data is distributed in separate packages in Bioconductor, whereas BiomaRt is used to retrieve annotation on demand. So if your downloaded information is too old, you probably have to switch to another mart.

[Sara]

thanks. I would like to download the annotation file for agilent gene for microarray gene expression data 8x60k human genome build GRCh38 ("agilent_sureprint_g3_ge_8x60k_v2.BiomaRt.GRCh38.txt"). A file named as below: I would like this information: Probe, Gene Names, gene description, chromosome, genomic coordiantes, gene coordiantes, gene type,.... I am adviced that Biomart R package can be used, I need to get help how to do that.

[jv]

What information do you needed updated? For example, do you want the genomic coordinates to be converted to a newer genome version? Do you want additional cross reference information for the genes?

What have you tried so far to get the updated information?

R readable format

human-readable files will be readable by R in addition to many non-human readable file formats, so this shouldn't be a concern/limitation.

[Sara]

Thank you. I do not have R cods. I would like to get the updated annotation file with information in my post. Parhaps using Biomart R package to get it? how? or directly download it? Any help is appreciated.

[Sara]

I use the R codes below, but gives me error "Error in is.data.frame(x) : object 'annotLookup' not found". I need the latest version genome build GRCH38 for microarray data. Also, how can I get the genomic coordinates, it seems that it is not available from attributes).

mart <- useMart('ENSEMBL_MART_ENSEMBL') 
mart <- useDataset('hsapiens_gene_ensembl', mart) 
annotLookup <- getBM(
  mart =
    mart,
  attributes =
    c(
      'agilent_sureprint_g3_ge_8x60k_v2',
      'wikigene_description',
      'ensembl_gene_id',
      'entrezgene_id',
      'gene_biotype',
      'external_gene_name'
    )
)

write.table(
  annotLookup,
  paste0(
    'Human_agilent_sureprint_g3_ge_8x60k_v2_',
    gsub("-","_", as.character(Sys.Date())),
    '.tsv'
  ),
  sep = '\t',
  row.names = FALSE,
  quote = FALSE
)