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Hi!
We are in need of characterising a new cell type (not tissue, pure cell).
We want to start by looking at the absolute expression values of genes.
(Going to compare to other cell types later using relative values).
I started out with Cufflinks, using FPKM, but I get a lot of short genes on the top of my list (miRNA, pseudo genes etc), I know thats because how Cufflinks "inflates" the FPKM of these genes. I also counted as CPM, but this is very biased by gene length...
Does anyone have an ide on whats the best normalisation method for looking at absolute expression levels?
What about:
1. CPM
2. Divide by gene length manually (how can I get these?)
3. Divide by library size
Thank you very much!
We are in need of characterising a new cell type (not tissue, pure cell).
We want to start by looking at the absolute expression values of genes.
(Going to compare to other cell types later using relative values).
I started out with Cufflinks, using FPKM, but I get a lot of short genes on the top of my list (miRNA, pseudo genes etc), I know thats because how Cufflinks "inflates" the FPKM of these genes. I also counted as CPM, but this is very biased by gene length...
Does anyone have an ide on whats the best normalisation method for looking at absolute expression levels?
What about:
1. CPM
2. Divide by gene length manually (how can I get these?)
3. Divide by library size
Thank you very much!