text: user506: I'm currently learning about Gene Set Enrichment Analysis (GSEA) in the hopes of using it in my analysis of differentially expressed genes, and I just had a few questions about the program, specifically about GSEAPreranked, which I need cleared up.
  
  On the ranked list needed for GSEA input, should the list include all genes, or only those that pass a certain threshold of significance (i.e. fold change higher than 2, p value less than 0.05, etc.)? Ideally I'd like to sort the genes by fold change alone as I don't trust my p values as much, so should I only include genes with high fold changes?
  I am comparing multiple conditions of disease with different treatments. Am I correct that GSEA only compares two conditions? If this is the case should I run GSEA for each control/treatment comparison? Would this be conventional?
  
  
  user2647: GSEAPreranked is a limited version of GSEA. 
  If your sample number is enough(more than 5,6 samples in each condition), you can use GSEA version. 
  Moreover, you can ask this question to the gsea-help google group. 
  
  user35: According to the GSEA documentation:
  
  we are recommending use of the GSEAPreranked tool for conducting gene
    set enrichment analysis of data derived from RNA-seq experiments
  
  Then more specifically to your question:
  
  Based on your differential expression analysis, rank your features and
    capture your ranking in an RNK-formatted file. The ranking metric can
    be whatever measure of differential expression you choose from the
    output of your selected DE tool. For example, cuffdiff provides the
    (base 2) log of the fold change.
  
  
  user48: You seem to refer to the GSEA provided by the Broad institute, (there are other GSEA algorithms). 
  1) You can provide whatever you wish, but if you want to know if those gene sets in which side of the ordered list are they, then provide all the list (of genes) you have.
  2) GSEA analyize if the order of a given list distributes in certain way the elements of another (unordered) list. In your case you would need to compute the GSEA for each treatment vs control comparison.
  
  user206: Use the following R package for Gene Set Enrichment analysis of RNA-seq data: seqGSEA
  There is another R package (fgsea) recently published called "Fast Gene Set Enrichment Analysis" by Alexey Sergushichev.
  
original_text: 506: <p>I'm currently learning about Gene Set Enrichment Analysis (<a href="http://software.broadinstitute.org/gsea/index.jsp" rel="nofollow noreferrer">GSEA</a>) in the hopes of using it in my analysis of differentially expressed genes, and I just had a few questions about the program, specifically about GSEAPreranked, which I need cleared up.</p>
  
  <ol>
  <li><p>On the ranked list needed for GSEA input, should the list include all genes, or only those that pass a certain threshold of significance (i.e. fold change higher than 2, p value less than 0.05, etc.)? Ideally I'd like to sort the genes by fold change alone as I don't trust my p values as much, so should I only include genes with high fold changes?</p></li>
  <li><p>I am comparing multiple conditions of disease with different treatments. Am I correct that GSEA only compares two conditions? If this is the case should I run GSEA for each control/treatment comparison? Would this be conventional?</p></li>
  </ol>
   2647: <p>GSEAPreranked is a limited version of GSEA. 
  If your sample number is enough(more than 5,6 samples in each condition), you can use GSEA version. 
  Moreover, you can ask this question to the gsea-help google group. </p>
   35: <p>According to the <a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ" rel="nofollow noreferrer">GSEA documentation</a>:</p>
  
  <blockquote>
    <p>we are recommending use of the GSEAPreranked tool for conducting gene
    set enrichment analysis of data derived from RNA-seq experiments</p>
  </blockquote>
  
  <p>Then more specifically to your question:</p>
  
  <blockquote>
    <p>Based on your differential expression analysis, rank your features and
    capture your ranking in an RNK-formatted file. The ranking metric can
    be whatever measure of differential expression you choose from the
    output of your selected DE tool. For example, cuffdiff provides the
    (base 2) log of the fold change.</p>
  </blockquote>
   48: <p>You seem to refer to the GSEA provided by the <a href="http://software.broadinstitute.org/gsea/index.jsp" rel="noreferrer">Broad institute</a>, (there are other GSEA algorithms). </p>
  
  <p>1) You can provide whatever you wish, but if you want to know if those gene sets in which side of the ordered list are they, then provide all the list (of genes) you have.</p>
  
  <p>2) GSEA analyize if the order of a given list distributes in certain way the elements of another (unordered) list. In your case you would need to compute the GSEA for each treatment vs control comparison.</p>
   206: <p>Use the following R package for Gene Set Enrichment analysis of RNA-seq data: <a href="https://www.bioconductor.org/packages/release/bioc/html/SeqGSEA.html" rel="nofollow noreferrer">seqGSEA</a></p>
  
  <p>There is another R package (<a href="https://bioconductor.org/packages/release/bioc/html/fgsea.html" rel="nofollow noreferrer">fgsea</a>) recently published called "Fast Gene Set Enrichment Analysis" by Alexey Sergushichev.</p>
  