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mkatari-bioinformatics-august-2013-deseq [2015/06/17 08:42] – mkatarimkatari-bioinformatics-august-2013-deseq [2015/08/21 14:13] (current) – mkatari
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 Then we will load the experimental design. An example is provided [[https://docs.google.com/file/d/0B172nc4dAaaOaE5fTVVhUHJKazg/edit?usp=sharing|here]]: Then we will load the experimental design. An example is provided [[https://docs.google.com/file/d/0B172nc4dAaaOaE5fTVVhUHJKazg/edit?usp=sharing|here]]:
 <code> <code>
-expdesign = read.table(pathToExpDesign)+expdesign = read.table("expdesign.txt")
 </code> </code>
  
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 An important part of DESeq is to estimate dispersion. This is simply a form of variance for the genes. An important part of DESeq is to estimate dispersion. This is simply a form of variance for the genes.
 <code> <code>
 +# if you have replicates do the following:
 cds = estimateDispersions( cds ) cds = estimateDispersions( cds )
 +### HOWEVER, If you have NO replicates, then try this
 +cds = estimateDispersions( cds, method="blind" , sharingMode = "fit-only" )
 </code> </code>
  
mkatari-bioinformatics-august-2013-deseq.1434530555.txt.gz · Last modified: by mkatari