Can anyone think of a clever way to compare transcriptomes? Let's say for example I've got a transcriptome (in the form of RPKM values for a number of transcripts) that I consider to be a gold standard, and I have two other experimental transcriptomes and I want to know which of my two experimental transcriptomes is more similar to my gold standard.
Should I just calculate a Pearson's correlation coefficient for those genes above some threshold for which I have RPKM data? Or set unexpressed transcripts to zero and run the same comparison? Any other ideas?
Thanks,
ucpete
Should I just calculate a Pearson's correlation coefficient for those genes above some threshold for which I have RPKM data? Or set unexpressed transcripts to zero and run the same comparison? Any other ideas?
Thanks,
ucpete
Comment