Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-18T12:09:02.667Z
Answers.LastActivityDate: 2017-08-18T12:09:02.667Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-21T17:11:48.763Z
Comments.Text: What type of comparison?
Comments.UserDisplayName: arup
Tags: <rna-seq><normalization><illumina>
Title: Analyzing Illumina Counts
ThreadText: # Analyzing Illumina Counts
  
  (Asked by: username_0 on 2017-08-18)
  
  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!
  
  **Tags:** rna-seq, normalization, illumina
  
  > **Comments:**
  > **username_1**: What type of comparison?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2017-08-18. Score: 5 | Accepted answer
  
  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.
  
  
  ---
  
  