edgeR: Time course RNA-seq experiments
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SuperDad • 0
@6c37bad3
Last seen 5 months ago
United States

The RNAseq examples in the section "Time course RNA-seq experiments of Drosophila melanogaster" are technical replicates. So, the reads can be summed by sumTechReps(). If I have biological replicates, how to sum the reads for the time course analysis (Natural cubic spline regression)? Thanks

edgeR • 647 views
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Yunshun Chen ▴ 870
@yunshun-chen-5451
Last seen 18 days ago
Australia

If the samples are biological replicates, you don't sum the reads (i.e., keep them as separate samples). You can generate an MDS plot to see if there is any sample effect (i.e., separation by sample in one of the dimensions). If so, you may also consider incorporating the sample effect into the design.

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Thanks for your prompt reply. Could you please help write a code example for biological replicates (assume the Drosophila melanogaster samples are biological replicates)? Thanks again!

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The edgeR manual covers everything to know. For other basic R code please take one of the many R tutorials out there in the web.

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