Oligo and Limma
I have just normalized a dataset with Oligo and annotated with it as well. I was wondering if anyone knows of any pipeline or command lines to do differential expression (gene by gene variance) with Limma on that normalized data. Thank you in advance.
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Is your normalised data of class ExpressionSet? If so, carry on and use limma. Look at the documentation for examples.
https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/intro.pdf
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