Answers.Body: <p>DESeq2 works for that.  Unless you literally have only two samples.</p>
  <p>There is <strong>no</strong> statistically sound way of analyzing DE genes with literally only two samples.  This is a bad experimental design, suitable for only the roughest of exploratory purposes.  Only the most obvious differences (that you probably knew already) are likely to be borne out in a legitimate experiment.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-11-03T06:07:38.290Z
Answers.LastActivityDate: 2021-12-04T06:09:26.820Z
Answers.LastEditDate: 2021-12-04T06:09:26.820Z
Answers.UserDisplayName: swbarnes2
Body: <p>We have an RNA seq taken from a the same tissue in two different developmental stages. We have one gene, with the number of reads from stage A and stage B, and we want to see which genes are differentially expressed.</p>
  <p>After performing RNA-seq, I am left with a CSV file containing a list of genes and the amount of reads in two different cell types. We have one list of genes, with the number of reads in Stage A in one column and the number of reads in Stage B in another column. We are looking to see what types of genes are differentially expressed in the two stages.</p>
  <p>I have used DESeq2, but I'm not sure if this is the best/correct to analyze what I am looking for.</p>
  <p>What is the best package to analyze the data for significant differential gene expression?</p>
  <p>Thanks</p>
  
Tags: <rna-seq><deseq2>
Title: Best R program to use for RNA seq analysis
ThreadText: # Best R program to use for RNA seq analysis
  
  (Asked by: username_0 on 2021-11-02)
  
  We have an RNA seq taken from a the same tissue in two different developmental stages. We have one gene, with the number of reads from stage A and stage B, and we want to see which genes are differentially expressed.
  
  After performing RNA-seq, I am left with a CSV file containing a list of genes and the amount of reads in two different cell types. We have one list of genes, with the number of reads in Stage A in one column and the number of reads in Stage B in another column. We are looking to see what types of genes are differentially expressed in the two stages.
  
  I have used DESeq2, but I'm not sure if this is the best/correct to analyze what I am looking for.
  
  What is the best package to analyze the data for significant differential gene expression?
  
  Thanks
  
  **Tags:** rna-seq, deseq2
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2021-11-03. Score: 1
  
  DESeq2 works for that. Unless you literally have only two samples.
  
  There is **no** statistically sound way of analyzing DE genes with literally only two samples. This is a bad experimental design, suitable for only the roughest of exploratory purposes. Only the most obvious differences (that you probably knew already) are likely to be borne out in a legitimate experiment.
  
  
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