I want to analyze RNA_Seq data that I found on the internet to practice. I found 8 RNA_Seq datasets (four different immune cells from mice and everytime two biological replicates). The goal of the analysis is to discover if there are genes that are differentially expressed.
I want to used edgeR to analyze the data. In order to order to do that, I need to specify a design matrix. There I am stuck. Cell type is one factor with 4 different levels in this analysis, but what about biological replicate? Should it also get an own factor with two levels?
I think biological replicate should not get a own factor, but I can not really explain why. It is a hunch.
Thanks in advance.
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written
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tmms •
3 answers
You might find this useful: C: DESeq2 proper design setting
If the all the replicates 1 were processed together and all the replicates 2 processed separately, then yes, you need to include that information as a factor because some variability could be explained by the level of the replicate. Otherwise, you should not include it.
Have a look on this paper .. https://rnajournal.cshlp.org/content/22/6/839.long
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