Question: RNA-Seq analysis and biological replicates.
0
gravatar for tmms
2.4 years ago by
tmms0
tmms0 wrote:

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.

ADD COMMENTlink modified 2.4 years ago by Carlo Yague4.4k • written 2.4 years ago by tmms0
1
gravatar for Macspider
2.4 years ago by
Macspider2.8k
Vienna - BOKU
Macspider2.8k wrote:

You might find this useful: C: DESeq2 proper design setting

ADD COMMENTlink written 2.4 years ago by Macspider2.8k
0
gravatar for Carlo Yague
2.4 years ago by
Carlo Yague4.4k
Belgium
Carlo Yague4.4k wrote:

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.

ADD COMMENTlink written 2.4 years ago by Carlo Yague4.4k
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