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Old 07-04-2011, 09:58 AM   #2
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

Have a look at the recently updated version of the DESeq vignette, where we use the data of Brooks et al. to demonstrate how to use GLMs to handle blocking factors such mixtures of different sequencing styles.

However, this probably does not apply to you. As you talk about only one sample, you don't want to compare anything anyway. And then, you might not even need replicates, depending on what you want to look for in your single sample. (And if you do need replicates, you are screwed anyway, as you don't have biological replicates.)
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