mkatari-bioinformatics-august-2013-deseq
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| mkatari-bioinformatics-august-2013-deseq [2015/06/17 08:42] – mkatari | mkatari-bioinformatics-august-2013-deseq [2026/07/14 06:11] (current) – external edit 127.0.0.1 | ||
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| Then we will load the experimental design. An example is provided [[https:// | Then we will load the experimental design. An example is provided [[https:// | ||
| < | < | ||
| - | expdesign = read.table(pathToExpDesign) | + | expdesign = read.table(" |
| </ | </ | ||
| Line 53: | Line 53: | ||
| 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. | ||
| < | < | ||
| + | # 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=" | ||
| </ | </ | ||
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