Question: How to remove the RIN (RNA integrity number) effect for RNA-seq data?
0
gravatar for Wayne Lee
11 months ago by
Wayne Lee10
Wayne Lee10 wrote:

Holle everyone! I am a beginner in RNA-seq data analysis. In my recently work, I face a problem: my RNA-seq data has significant correlation with sample's RIN (RNA integrity number), and I want to remove this effect. Some papers indicate that one can use a linear model to normalize this technical covariate, but I do not know how to do it. If anybody can help me about this? Or if there have any other methods can sovel this problem? Thank you very much!

rna-seq normalization • 723 views
ADD COMMENTlink modified 11 months ago by Michele Busby1.9k • written 11 months ago by Wayne Lee10
4
gravatar for Devon Ryan
11 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Don't bother actually removing it, just put it in as a covariate in your model.

ADD COMMENTlink written 11 months ago by Devon Ryan89k

Thank you answer this simple questure! But, I don't quite understand what your mean. Can you tell me more details? Or can you supply me some material or papers about this? thank you!

ADD REPLYlink written 11 months ago by Wayne Lee10

You can google "DESeq2 nuisance covariate" for various examples.

ADD REPLYlink written 11 months ago by Devon Ryan89k

THX, it's helpful !!

ADD REPLYlink written 11 months ago by Wayne Lee10
0
gravatar for Michele Busby
11 months ago by
Michele Busby1.9k
United States
Michele Busby1.9k wrote:

You may want to try looking at the supplements for the GTEx papers. They did a lot of work on that. It also depends a lot on the protocol. If it is PolyA selected you will get biases against short genes because you will lose the 5' end. If it is RNA depleted or hybrid capture your bias will be different, so make sure the model you are looking at is applicable. The GTEx, I believe, was mostly poly-A kits.

ADD COMMENTlink written 11 months ago by Michele Busby1.9k
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