Hi all,
I have RNA-seq data for 3 conditions (with biological replicates), and I`m hoping to investigate how the exon usage varies across conditions. I am using testGeneForDEU and spliceVariants in DEXSeq and edgeR repsectively to identify genes that show evidence of differential exon usage. I want to go a step further and compare exonic expression across conditions. For example, I want to see if behavior of a gene for condition 1 is similar to condition 2 or 3.
So if an exon is expressed more in condition 2, and little in condition 3, which way does condition 1 behave, and maybe classify it as 2-like, 3-like or mean of 2 and 3? Is there a way to statistically look at this? Both packages provide nice way to visualize this through plotexonUsage and plotDEXSeq.
Thanks,
Al
I have RNA-seq data for 3 conditions (with biological replicates), and I`m hoping to investigate how the exon usage varies across conditions. I am using testGeneForDEU and spliceVariants in DEXSeq and edgeR repsectively to identify genes that show evidence of differential exon usage. I want to go a step further and compare exonic expression across conditions. For example, I want to see if behavior of a gene for condition 1 is similar to condition 2 or 3.
So if an exon is expressed more in condition 2, and little in condition 3, which way does condition 1 behave, and maybe classify it as 2-like, 3-like or mean of 2 and 3? Is there a way to statistically look at this? Both packages provide nice way to visualize this through plotexonUsage and plotDEXSeq.
Thanks,
Al
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