text: user4293: I've downloaded this GSE43013 dataset using GEOquery in R. My understanding is that it contains expression data from liver, kidney, and brain for multiple species. I would like to produce gene expression tables for each species and tissue type. The goal would then be to perform PCA and regression analyses to see if there is a relationship between expression of certain genes and e.g. taxonomic position, diet, etc.
  However, I have never worked with gene expression data before so I have very little understanding of the GSE file. I have failed to extract any kind of expression data from the file. Solutions that I have found online do not seem to be working for this dataset (for example producing empty tables where I assume there would normally be data on expression levels). Because of my inexperience I cannot determine why they are not working in this situation.
  I would appreciate some help in understanding the format of this file, but most importantly, in figuring out how to pull expression data from it, if that is possible.
  EDIT: I still haven't managed to pull data from the GSE file, but looking through the samples associated with the data set (such as this one), I can see that there are files formatted like this:
  mus.lv.3
  ENSMUSG00000000001  26.3376
  ENSMUSG00000000003  0
  ENSMUSG00000000028  0.501533
  ENSMUSG00000000031  0.116078
  I assume that the values in the left column refer to specific genes. Perhaps the values in the right column represent expression intensity? If so, would these values be normalized and comparable between species as they are?
  
  user4306: Assuming that you have downloaded processed file, according to your link, it is either plain text (compressed) or GTF. If you would have plain text you probably would have posted a snapshot or sample of it, so I assume you have the GTF. According to format description for GTF-files: 
  
  Format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. 
  The 9 columns (or fields) are tab-separated and all fields contain a value (missing/NA-values are usually denoted with "."). 
  Fields are: 
  
  
  seqname - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seqname must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below.
  source - name of the program that generated this feature, or the data source (database or project name)
  feature - feature type name, e.g. Gene, Variation, Similarity
  start - Start position of the feature, with sequence numbering starting at 1.
  end - End position of the feature, with sequence numbering starting at 1.
  score - A floating point value.
  strand - defined as + (forward) or - (reverse).
  frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..
  attribute - A semicolon-separated list of tag-value pairs, providing additional information about each feature.
  
  
  You can find more information on it here and here. 
  IF you don´t have the file and just have the query output, you probably will find the answer here, where extraction of expression data has been discussed in more detail.
  
original_text: 4293: <p>I've downloaded this <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43013" rel="nofollow noreferrer">GSE43013</a> dataset using GEOquery in R. My understanding is that it contains expression data from liver, kidney, and brain for multiple species. I would like to produce gene expression tables for each species and tissue type. The goal would then be to perform PCA and regression analyses to see if there is a relationship between expression of certain genes and e.g. taxonomic position, diet, etc.</p>
  
  <p>However, I have never worked with gene expression data before so I have very little understanding of the GSE file. I have failed to extract any kind of expression data from the file. Solutions that I have found online do not seem to be working for this dataset (for example producing empty tables where I assume there would normally be data on expression levels). Because of my inexperience I cannot determine why they are not working in this situation.</p>
  
  <p>I would appreciate some help in understanding the format of this file, but most importantly, in figuring out how to pull expression data from it, if that is possible.</p>
  
  <p>EDIT: I still haven't managed to pull data from the GSE file, but looking through the samples associated with the data set (such as <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1055020" rel="nofollow noreferrer">this one</a>), I can see that there are files formatted like this:</p>
  
  <p>mus.lv.3</p>
  
  <p>ENSMUSG00000000001  26.3376</p>
  
  <p>ENSMUSG00000000003  0</p>
  
  <p>ENSMUSG00000000028  0.501533</p>
  
  <p>ENSMUSG00000000031  0.116078</p>
  
  <p>I assume that the values in the left column refer to specific genes. Perhaps the values in the right column represent expression intensity? If so, would these values be normalized and comparable between species as they are?</p>
   4306: <p>Assuming that you have downloaded processed file, according to your link, it is either plain text (compressed) or GTF. If you would have plain text you probably would have posted a snapshot or sample of it, so I assume you have the GTF. According to format description for GTF-files: </p>
  
  <ul>
  <li>Format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. </li>
  <li>The 9 columns (or fields) are tab-separated and all fields contain a value (missing/NA-values are usually denoted with "."). </li>
  <li>Fields are: 
  
  <ol>
  <li><strong>seqname</strong> - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seqname must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below.</li>
  <li><strong>source</strong> - name of the program that generated this feature, or the data source (database or project name)</li>
  <li><strong>feature</strong> - feature type name, e.g. Gene, Variation, Similarity</li>
  <li><strong>start</strong> - Start position of the feature, with sequence numbering starting at 1.</li>
  <li><strong>end</strong> - End position of the feature, with sequence numbering starting at 1.</li>
  <li><strong>score</strong> - A floating point value.</li>
  <li><strong>strand</strong> - defined as + (forward) or - (reverse).</li>
  <li><strong>frame</strong> - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..</li>
  <li><strong>attribute</strong> - A semicolon-separated list of tag-value pairs, providing additional information about each feature.</li>
  </ol></li>
  </ul>
  
  <p>You can find more information on it <a href="http://gmod.org/wiki/GFF2" rel="nofollow noreferrer">here</a> and <a href="https://www.ensembl.org/info/website/upload/gff.html" rel="nofollow noreferrer">here</a>. </p>
  
  <p>IF you don´t have the file and just have the query output, you probably will find the answer <a href="https://bioinformatics.stackexchange.com/questions/2408/extracting-expression-data-from-gse-dataset-downloaded-from-geo">here</a>, where extraction of expression data has been discussed in more detail.</p>
  