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Old 11-07-2013, 07:06 AM   #3
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Originally Posted by davidblaney View Post
The FPKM values for the genes are a sum of the FPKM values found for transcripts of that gene... so I guess you could expect differing values come from the difference in transcripts and the reads/fragments covering them.

To test I would look at the transcripts FPKM values for each gene that have the same loci.
The FPKM values for multiple transcripts with identical coordinates are very different. Additonally, they can even be called significantly different between two samples and in different directions.
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