Answers.Body: <p>Hi An Ignorant Wanderer,</p>
  <p>Yes, you're right - ENST00000414213 is a deprecated ID from Ensembl release 75.</p>
  <p><a href="https://www.ensembl.org/Homo_sapiens/Transcript/Idhistory?t=ENST00000414213" rel="nofollow noreferrer">https://www.ensembl.org/Homo_sapiens/Transcript/Idhistory?t=ENST00000414213</a></p>
  <p>To convert a list of IDs from GRCh37, you will need to use the GRCh37 dataset. You can do this using the following documentation/example:
  <a href="https://www.ensembl.org/info/data/biomart/biomart_r_package.html" rel="nofollow noreferrer">https://www.ensembl.org/info/data/biomart/biomart_r_package.html</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-11-09T12:09:51.040Z
Answers.LastActivityDate: 2022-11-09T12:09:51.040Z
Answers.UserDisplayName: Ben_Moore
Body: <p>When I run the following R code to convert Ensembl transcript IDs to gene names and Ensembl gene IDs:</p>
  <pre><code>mart &lt;- useMart(&quot;ensembl&quot;, dataset = &quot;hsapiens_gene_ensembl&quot;)
  ensemble2gene &lt;- getBM(attributes=c(&quot;ensembl_transcript_id&quot;, 
                                      &quot;external_gene_name&quot;,
                                      &quot;ensembl_gene_id&quot;),
                         filters = &quot;ensembl_transcript_id&quot;,
                         values = as.list(transcripts), 
                         mart = mart)
  </code></pre>
  <p>some of rows returned have NA values for both the gene name and Ensembl gene ID. This is a bit odd because for example, one of the transcript IDs with missing gene IDs is ENST00000414213 but when I google it, I find that it corresponds to gene ENSG00000235143 (according to <a href="http://genome-euro.ucsc.edu/cgi-bin/hgGene?hgg_gene=ENST00000431202.1&amp;hgg_chrom=chr1&amp;hgg_start=30858157&amp;hgg_end=30860254&amp;hgg_type=knownGene&amp;db=hg38" rel="nofollow noreferrer">this</a>). Why am I getting missing results in <code>getBM</code> then? Is it because maybe the transcript is from an old version of the database? If so, is that the only reason or are there other reasons this could be happening?</p>
  
Tags: <r><ensembl><biomart>
Title: Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?
ThreadText: # Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?
  
  (Asked by: username_0 on 2022-11-05)
  
  When I run the following R code to convert Ensembl transcript IDs to gene names and Ensembl gene IDs:
  
  ```
  mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
  ensemble2gene <- getBM(attributes=c("ensembl_transcript_id", 
                                      "external_gene_name",
                                      "ensembl_gene_id"),
                         filters = "ensembl_transcript_id",
                         values = as.list(transcripts), 
                         mart = mart)
  
  ```
  
  some of rows returned have NA values for both the gene name and Ensembl gene ID. This is a bit odd because for example, one of the transcript IDs with missing gene IDs is ENST00000414213 but when I google it, I find that it corresponds to gene ENSG00000235143 (according to [this](http://genome-euro.ucsc.edu/cgi-bin/hgGene?hgg_gene=ENST00000431202.1&hgg_chrom=chr1&hgg_start=30858157&hgg_end=30860254&hgg_type=knownGene&db=hg38)). Why am I getting missing results in `getBM` then? Is it because maybe the transcript is from an old version of the database? If so, is that the only reason or are there other reasons this could be happening?
  
  **Tags:** r, ensembl, biomart
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-11-09. Score: 0 | Accepted answer
  
  Hi An Ignorant username_0,
  
  Yes, you're right - ENST00000414213 is a deprecated ID from Ensembl release 75.
  
  <https://www.ensembl.org/Homo_sapiens/Transcript/Idhistory?t=ENST00000414213>
  
  To convert a list of IDs from GRCh37, you will need to use the GRCh37 dataset. You can do this using the following documentation/example:
  <https://www.ensembl.org/info/data/biomart/biomart_r_package.html>
  
  
  ---
  
  