Answers.Body: <p>If you print <code>G_list</code>, you'll see this half way down:</p>
  
  <pre><code>1 ENSMUSG00000060550      15018      H2-Q7      Mus musculus histocompatibility 2, Q region locus 9 (H2-Q9), mRNA. [Source:RefSeq mRNA;Acc:NM_001201460]
  2 ENSMUSG00000060550     110558      H2-Q7      Mus musculus histocompatibility 2, Q region locus 9 (H2-Q9), mRNA. [Source:RefSeq mRNA;Acc:NM_001201460]
  </code></pre>
  
  <p>So there are two <code>entrez</code> ids that map to the same <code>Ensembl</code> id. <a href="https://www.ncbi.nlm.nih.gov/gene/?term=110558" rel="noreferrer">One</a> of them maps to an alt locus.</p>
  
  <p>If you exclude <code>"entrezgene"</code> from the query, you'll get 30 results.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-16T20:28:52.957Z
Answers.LastActivityDate: 2018-04-16T20:28:52.957Z
Answers.UserDisplayName: heathobrien
Body: <p>I am supplying 30 ensembl ids into BioMart, but somehow it returns 31 result. What is going wrong here?
  Here you can see the code:</p>
  
  <pre><code>library('biomaRt')
  mart &lt;- useDataset("mmusculus_gene_ensembl", useMart("ensembl"))
  genes &lt;- rownames(mat)
  G_list &lt;- getBM(filters= "ensembl_gene_id", attributes= 
  c("ensembl_gene_id","entrezgene", 
  "mgi_symbol","description"),values=genes,mart= mart)
  </code></pre>
  
  <p>genes list is the following one: </p>
  
  <pre><code>[1] "ENSMUSG00000097971" "ENSMUSG00000097582" "ENSMUSG00000061808" "ENSMUSG00000097206"
  [5] "ENSMUSG00000022425" "ENSMUSG00000094708" "ENSMUSG00000095937" "ENSMUSG00000032484"
  [9] "ENSMUSG00000060550" "ENSMUSG00000073409" "ENSMUSG00000026822" "ENSMUSG00000056071"
  [13] "ENSMUSG00000035299" "ENSMUSG00000045932" "ENSMUSG00000006154" "ENSMUSG00000032496"
  [17] "ENSMUSG00000040809" "ENSMUSG00000032690" "ENSMUSG00000055322" "ENSMUSG00000066443"
  [21] "ENSMUSG00000005089" "ENSMUSG00000073489" "ENSMUSG00000005800" "ENSMUSG00000034855"
  [25] "ENSMUSG00000029417" "ENSMUSG00000029561" "ENSMUSG00000021843" "ENSMUSG00000020108"
  [29] "ENSMUSG00000037849" "ENSMUSG00000066861"
  </code></pre>
  
  <p>As you can see I have here 30 genes, but BioMart returns:</p>
  
  <pre><code>&gt; G_list$mgi_symbol
  [1] "Slc1a2"  "Mmp8"    "Eps8l1"  "Ddit4"   "Ktn1"    "Enpp2"   "Lcn2"    "Cxcl9"  
  [9] "Oasl2"   "Ngp"     "Ltf"     "Oas2"    "Cxcl10"  "Mid1"    "Ifi206"  "Chil3"  
  [17] "Ifit2"   "Tns1"    "S100a9"  "H2-Q7"   "H2-Q7"   "Ttr"     "Gm10163" "Oas1g"  
  [25] "H2-Q6"   "Ifi204"  "Gm10359" "Gm12671" "Gm26699" "Gm26527" "Gm26917"
  </code></pre>
  
Tags: <rna-seq><biomart>
Title: BioMart returns one more item
ThreadText: # BioMart returns one more item
  
  (Asked by: username_0 on 2018-04-16)
  
  I am supplying 30 ensembl ids into BioMart, but somehow it returns 31 result. What is going wrong here?
  Here you can see the code:
  
  ```
  library('biomaRt')
  mart <- useDataset("mmusculus_gene_ensembl", useMart("ensembl"))
  genes <- rownames(mat)
  G_list <- getBM(filters= "ensembl_gene_id", attributes= 
  c("ensembl_gene_id","entrezgene", 
  "mgi_symbol","description"),values=genes,mart= mart)
  
  ```
  
  genes list is the following one:
  
  ```
  [1] "ENSMUSG00000097971" "ENSMUSG00000097582" "ENSMUSG00000061808" "ENSMUSG00000097206"
  [5] "ENSMUSG00000022425" "ENSMUSG00000094708" "ENSMUSG00000095937" "ENSMUSG00000032484"
  [9] "ENSMUSG00000060550" "ENSMUSG00000073409" "ENSMUSG00000026822" "ENSMUSG00000056071"
  [13] "ENSMUSG00000035299" "ENSMUSG00000045932" "ENSMUSG00000006154" "ENSMUSG00000032496"
  [17] "ENSMUSG00000040809" "ENSMUSG00000032690" "ENSMUSG00000055322" "ENSMUSG00000066443"
  [21] "ENSMUSG00000005089" "ENSMUSG00000073489" "ENSMUSG00000005800" "ENSMUSG00000034855"
  [25] "ENSMUSG00000029417" "ENSMUSG00000029561" "ENSMUSG00000021843" "ENSMUSG00000020108"
  [29] "ENSMUSG00000037849" "ENSMUSG00000066861"
  
  ```
  
  As you can see I have here 30 genes, but BioMart returns:
  
  ```
  > G_list$mgi_symbol
  [1] "Slc1a2"  "Mmp8"    "Eps8l1"  "Ddit4"   "Ktn1"    "Enpp2"   "Lcn2"    "Cxcl9"  
  [9] "Oasl2"   "Ngp"     "Ltf"     "Oas2"    "Cxcl10"  "Mid1"    "Ifi206"  "Chil3"  
  [17] "Ifit2"   "Tns1"    "S100a9"  "H2-Q7"   "H2-Q7"   "Ttr"     "Gm10163" "Oas1g"  
  [25] "H2-Q6"   "Ifi204"  "Gm10359" "Gm12671" "Gm26699" "Gm26527" "Gm26917"
  
  ```
  
  **Tags:** rna-seq, biomart
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-04-16. Score: 6 | Accepted answer
  
  If you print `G_list`, you'll see this half way down:
  
  ```
  1 ENSMUSG00000060550      15018      H2-Q7      Mus musculus histocompatibility 2, Q region locus 9 (H2-Q9), mRNA. [Source:RefSeq mRNA;Acc:NM_001201460]
  2 ENSMUSG00000060550     110558      H2-Q7      Mus musculus histocompatibility 2, Q region locus 9 (H2-Q9), mRNA. [Source:RefSeq mRNA;Acc:NM_001201460]
  
  ```
  
  So there are two `entrez` ids that map to the same `Ensembl` id. [One](https://www.ncbi.nlm.nih.gov/gene/?term=110558) of them maps to an alt locus.
  
  If you exclude `"entrezgene"` from the query, you'll get 30 results.
  
  
  ---
  
  