I have got my expression matrix and downloaded the official annotation .csv document. The problem is there shows different resources of annotation information in my mrna_assignment column, include RefSeq, Ensembl, lncRNAWiki, AceView and so on. Some of probes have only NM_/NR_, some of them have only ENST, and the others have neither.

 > head(ann.df$gene_id,1)
[1] NR_046018 // RefSeq // Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 (DDX11L1), non-coding RNA. // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000002844 // Havana transcript // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1[gene_biotype:transcribed_unprocessed_pseudogene transcript_biotype:transcribed_unprocessed_pseudogene] // chr1 // 100 // 100 // 0 // --- // 0 /// OTTHUMT00000362751 // Havana transcript // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1[gene_biotype:transcribed_unprocessed_pseudogene transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000450305 // ENSEMBL // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 [gene_biotype:transcribed_unprocessed_pseudogene transcript_biotype:transcribed_unprocessed_pseudogene] // chr1 // 100 // 100 // 0 // --- // 0 /// ENST00000456328 // ENSEMBL // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 [gene_biotype:transcribed_unprocessed_pseudogene transcript_biotype:processed_transcript] // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000001 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000001 // NONCODE // Non-coding transcript identified by NONCODE: Linc // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000002 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000002 // NONCODE // Non-coding transcript identified by NONCODE: Linc // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000003 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000003 // NONCODE // Non-coding transcript identified by NONCODE: Linc // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000004 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000004 // NONCODE // Non-coding transcript identified by NONCODE: Linc // chr1 // 100 // 100 // 0 // --- // 0
135757 Levels: --- // --- // Antigenomic background control // --- // --- // --- // --- // --- // --- ...

To further analyze my data, I have to transfer this annotation information into the same ENST form, and I downloaded .gtf documents from Ensembl and RefSeq respectively. Then I found there are still many probes that can not be transferred because they are not RefSeq or Ensembl.

ann.df$gene_id <- sub ('//.*', '', ann.df$gene_id)
head(ann.df)
        probeset_id chromosome_name start   end       locus.type                    gene_id
1 TC0100006432.hg.1            chr1 11869 14412 Multiple_Complex                 NR_046018 
2 TC0100006433.hg.1            chr1 28046 29178           Coding spopoybu.aAug10-unspliced 
3 TC0100006434.hg.1            chr1 29554 31109 Multiple_Complex                 NR_036267 
4 TC0100006435.hg.1            chr1 52473 53312       Pseudogene        OTTHUMT00000471235 
5 TC0100006436.hg.1            chr1 62948 63887 Multiple_Complex           ENST00000492842

Then I consider using my locus information to match the ENST, however, the biomaRt package use filter as a list form and the locus information of my whole df is too big to be transferred as a list.

ensembl <- useMart ('ensembl', dataset = 'hsapiens_gene_ensembl')
tem <- getBM (ensembl, attributes = c(
    "hgnc_symbol",
    "ensembl_gene_id",
    "gene_biotype",
    "external_gene_name"),
  filter = c('chromosome_name','start','end')
  values = ann.df$gene_id,
  uniqueRows =TRUE)

I don't know hoiw to deal with it, now. Please help me.