text: user1226: I'm pretty new to all of this--forgive me if this is a simple question.
  When I download illumina counts from GEO (like the supplementary file in 
  GSE89225). Can I do comparisons directly on that file? Is there some normalization procedure I should go through?
  Thanks!
  
  user77: The counts files for GSE89225 is the output of HTSeq-count as a large matrix. Unless you are developing a differential expression package yourself you should not attempt to directly use this. Rather, you should load it into R and use packages such as DESeq2, edgeR, or limma (those are the most popular ones).
  For convenience, in DESeq2 you would want the DESeqDatasetFromMatrix() function after loading this.
  
original_text: 1226: <p>I'm pretty new to all of this--forgive me if this is a simple question.</p>
  
  <p>When I download illumina counts from GEO (like the supplementary file in 
  GSE89225). Can I do comparisons directly on that file? Is there some normalization procedure I should go through?</p>
  
  <p>Thanks!</p>
   77: <p>The counts files for GSE89225 is the output of HTSeq-count as a large matrix. Unless you are developing a differential expression package yourself you should not attempt to directly use this. Rather, you should load it into R and use packages such as DESeq2, edgeR, or limma (those are the most popular ones).</p>
  
  <p>For convenience, in DESeq2 you would want the <code>DESeqDatasetFromMatrix()</code> function after loading this.</p>
  