text: user1782: I am new to bioinformatics, my background is in Electrical Engineering. I am trying to convert Affymetrix Cotton Probe IDs to gene symbols. I have a gene expression dataset and I need the expressions for only certain genes. So in the dataset, I have a probe id such as Ghi.10301.1.S1_s_at, how can I get the gene symbol associated with it? Thanks
  EDIT: This is the specific dataset I am looking at 
  https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50770
  
  user181: Your dataset was produced on a microarray. The probe IDs in the FASTA file are similar to read IDs produced from other NGS experiments like RNA-Seq. According to the workflow provided by Ensembl the first step is to align your reads to a reference. You'll only keep the reads that match the reference completely. Once the probes are aligned you'll be able to quantify the number of reads mapping to the gene that the probe was designed to attract.
  I did find a file providing the database entries associated with each probe ID (one of which is the ID you provided) for the Affymetrix Cotton Genome Array.
  
  
  user194: The first stop for decoding probe IDs for a microarray platform is usually the GEO Platform Description: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL8672
  This description contains a table of annotation, and is provided (in this instance) by the array manufacturer. You can view, or download, the full table: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GPL8672&id=1538&db=GeoDb_blob35
  GEO Platform annotations do date, and so for up-to-date annotations, download from NetAffx: http://www.affymetrix.com/support/technical/byproduct.affx?product=cotton
  The most recent annotations (dated 2016-04-13) are available here: http://www.affymetrix.com/Auth/analysis/downloads/na36/ivt/Cotton.na36.annot.csv.zip.
  For the example in your question, looking at this probe in the CSV: 
  "Ghi.10301.1.S1_s_at","Cotton Genome Array","Gossypium hirsutum","Mar 30, 2016","Consensus sequence","GenBank","Ghi.10301.1","gb:DT050231 /DB_XREF=gi:72275634 /DB_XREF=COT_DW_H07 /TID=Ghi.10301.1 /CNT=21 /FEA=EST /TIER=ConsEnd /STK=1 /UG=Ghi.10301 /UG_TITLE=Transcribed locus, moderately similar to NP_568148.1 ubiquitin conjugating enzyme ubiquitin-like activating enzyme (Arabidopsis thaliana) /REP_ORG=G. hirsutum","DT050231","Ghi.10301","Ghi.10301","---","---","---","---","---","est","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","This probe set was annotated using the Accession mapped clusters based pipeline to a UniGene identifier using 21 transcripts. // false // Accession mapped clusters // E","AI730871,DN803875,DR452973,DR457278,DT050231,DT545642,DT546719,DT546982,DT546983,DT547780,DT547781,DT555433,DT559909,DT564450,DT566924,DT569293,DT569974,DT571307,DT571318,DT571472,DT573548","AI730871 // /DB_XREF=BNLGHi8130 // gb // --- // --- /// DN803875 // /DB_XREF=G.hir-8-10 DAA bolls drought stressed751 // gb // --- // --- /// DR452973 // /DB_XREF=CM008C10 // gb // --- // --- /// DR457278 // /DB_XREF=CM053F01 // gb // --- // --- /// DT050231 // /DB_XREF=COT_DW_H07 // gb // --- // --- /// DT545642 // /DB_XREF=EST1056282 // gb // --- // --- /// DT546719 // /DB_XREF=EST1057359 // gb // --- // --- /// DT546982 // /DB_XREF=EST1057622 // gb // --- // --- /// DT546983 // /DB_XREF=EST1057623 // gb // --- // --- /// DT547780 // /DB_XREF=EST1058420 // gb // --- // --- /// DT547781 // /DB_XREF=EST1058421 // gb // --- // --- /// DT555433 // /DB_XREF=EST1066073 // gb // --- // --- /// DT559909 // /DB_XREF=EST1070549 // gb // --- // --- /// DT564450 // /DB_XREF=EST1075090 // gb // --- // --- /// DT566924 // /DB_XREF=EST1077564 // gb // --- // --- /// DT569293 // /DB_XREF=EST1079933 // gb // --- // --- /// DT569974 // /DB_XREF=EST1080614 // gb // --- // --- /// DT571307 // /DB_XREF=EST1081947 // gb // --- // --- /// DT571318 // /DB_XREF=EST1081958 // gb // --- // --- /// DT571472 // /DB_XREF=EST1082112 // gb // --- // --- /// DT573548 // /DB_XREF=EST1084188 // gb // --- // ---","---"
  
  
original_text: 1782: <p>I am new to bioinformatics, my background is in Electrical Engineering. I am trying to convert Affymetrix Cotton Probe IDs to gene symbols. I have a gene expression dataset and I need the expressions for only certain genes. So in the dataset, I have a probe id such as Ghi.10301.1.S1_s_at, how can I get the gene symbol associated with it? Thanks</p>
  
  <p>EDIT: This is the specific dataset I am looking at 
  <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50770" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50770</a></p>
   181: <p>Your dataset was produced on a microarray. The probe IDs in the FASTA file are similar to read IDs produced from other NGS experiments like RNA-Seq. According to the workflow provided by Ensembl the first step is to align your reads to a reference. You'll only keep the reads that match the reference completely. Once the probes are aligned you'll be able to quantify the number of reads mapping to the gene that the probe was designed to attract.</p>
  
  <p>I did find <a href="https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8672/A-GEOD-8672.adf.txt" rel="nofollow noreferrer">a file</a> providing the database entries associated with each probe ID (one of which is the ID you provided) for the Affymetrix Cotton Genome Array.</p>
  
  <p><a href="https://i.stack.imgur.com/fDUUK.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/fDUUK.png" alt="probe microarray workflow"></a></p>
   194: <p>The first stop for decoding probe IDs for a microarray platform is usually the GEO Platform Description: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL8672" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL8672</a></p>
  
  <p>This description contains a table of annotation, and is provided (in this instance) by the array manufacturer. You can view, or download, the full table: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&amp;acc=GPL8672&amp;id=1538&amp;db=GeoDb_blob35" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&amp;acc=GPL8672&amp;id=1538&amp;db=GeoDb_blob35</a></p>
  
  <p>GEO Platform annotations do date, and so for up-to-date annotations, download from NetAffx: <a href="http://www.affymetrix.com/support/technical/byproduct.affx?product=cotton" rel="nofollow noreferrer">http://www.affymetrix.com/support/technical/byproduct.affx?product=cotton</a></p>
  
  <p>The most recent annotations (dated 2016-04-13) are available here: <a href="http://www.affymetrix.com/Auth/analysis/downloads/na36/ivt/Cotton.na36.annot.csv.zip" rel="nofollow noreferrer">http://www.affymetrix.com/Auth/analysis/downloads/na36/ivt/Cotton.na36.annot.csv.zip</a>.</p>
  
  <p>For the example in your question, looking at this probe in the CSV: </p>
  
  <pre><code>"Ghi.10301.1.S1_s_at","Cotton Genome Array","Gossypium hirsutum","Mar 30, 2016","Consensus sequence","GenBank","Ghi.10301.1","gb:DT050231 /DB_XREF=gi:72275634 /DB_XREF=COT_DW_H07 /TID=Ghi.10301.1 /CNT=21 /FEA=EST /TIER=ConsEnd /STK=1 /UG=Ghi.10301 /UG_TITLE=Transcribed locus, moderately similar to NP_568148.1 ubiquitin conjugating enzyme ubiquitin-like activating enzyme (Arabidopsis thaliana) /REP_ORG=G. hirsutum","DT050231","Ghi.10301","Ghi.10301","---","---","---","---","---","est","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","This probe set was annotated using the Accession mapped clusters based pipeline to a UniGene identifier using 21 transcripts. // false // Accession mapped clusters // E","AI730871,DN803875,DR452973,DR457278,DT050231,DT545642,DT546719,DT546982,DT546983,DT547780,DT547781,DT555433,DT559909,DT564450,DT566924,DT569293,DT569974,DT571307,DT571318,DT571472,DT573548","AI730871 // /DB_XREF=BNLGHi8130 // gb // --- // --- /// DN803875 // /DB_XREF=G.hir-8-10 DAA bolls drought stressed751 // gb // --- // --- /// DR452973 // /DB_XREF=CM008C10 // gb // --- // --- /// DR457278 // /DB_XREF=CM053F01 // gb // --- // --- /// DT050231 // /DB_XREF=COT_DW_H07 // gb // --- // --- /// DT545642 // /DB_XREF=EST1056282 // gb // --- // --- /// DT546719 // /DB_XREF=EST1057359 // gb // --- // --- /// DT546982 // /DB_XREF=EST1057622 // gb // --- // --- /// DT546983 // /DB_XREF=EST1057623 // gb // --- // --- /// DT547780 // /DB_XREF=EST1058420 // gb // --- // --- /// DT547781 // /DB_XREF=EST1058421 // gb // --- // --- /// DT555433 // /DB_XREF=EST1066073 // gb // --- // --- /// DT559909 // /DB_XREF=EST1070549 // gb // --- // --- /// DT564450 // /DB_XREF=EST1075090 // gb // --- // --- /// DT566924 // /DB_XREF=EST1077564 // gb // --- // --- /// DT569293 // /DB_XREF=EST1079933 // gb // --- // --- /// DT569974 // /DB_XREF=EST1080614 // gb // --- // --- /// DT571307 // /DB_XREF=EST1081947 // gb // --- // --- /// DT571318 // /DB_XREF=EST1081958 // gb // --- // --- /// DT571472 // /DB_XREF=EST1082112 // gb // --- // --- /// DT573548 // /DB_XREF=EST1084188 // gb // --- // ---","---"
  </code></pre>
  