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Hi,

proteins are synthetised from transcripts, not from genes, so I wouldn't use gene DE. It can become quite tricky to interpret these for some alternative transcripts.

Beast, Leonor.

On 28/07/12 18:06, i b wrote:

Hi, I am a bit confused about two outputs of cuffdiff: If I want to see if two samples, e.g. treated and un-treated express similar protein levels, what would be best to look at gene differential expression or transcript diff. expression?

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