Hello everyone, I had a question on how to gain quantile normalized data with my current FPKM and raw data. Is there an R code for quantile normalization to do DEG analysis? Any help would be greatly appreciated! Thank you.
Hello francis24kim!
Questions similar to yours can already be found at:
Rnaseq Fpkm Quantile Normalization
Quantile normalizing prior to or after TPM scaling?
quantile normalization for normalized values
Differences between FPKM and FPKM-UQ files in gene expression analysis
and then on how to do DEG with normalized data:
gene expression analysis using RNA seq data
How to do FPKM differential analysis?
Comparing FPKM values in different genes
You want to read about "limma-trend" pipeline as well. The relevant thread over at Bioconductor from the author of limma is here: https://support.bioconductor.org/p/56275/
Please also search support.bioconductor.org which has plenty of posts on that.
We have closed your question to allow us to keep similar content in the same thread.
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Cheers!
Thank you ATpoint, your answer was very helpful! I'll try and share anything new that comes up during my attempt. Cheers!
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