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Old 08-17-2015, 08:57 AM   #2
csmatyi
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Location: Nebraska

Join Date: Oct 2011
Posts: 25
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Hello everybody,

I have a line from genes.fpkm_tracking from cuffdiff output:

XLOC_000001 - - XLOC_000001 NM_008866 TSS1 chr1:4807892-4846735 - - 18.3357 13.5137 23.1577 OK 18.0846 13.4121 22.7572 OK

Here the aggregated control sample value is 18.3357

However, from the 3 control transcript.gtf files I have these 3 values:

../Nsg1-Hip_tophat/cufflinks_output_gtf/genes.fpkm_tracking:NM_008866 - - NM_008866 - - chr1:4807892-4846735 - - 16.1344 13.3363 18.9325 OK
../Nsg2-Hip_tophat/cufflinks_output_gtf/genes.fpkm_tracking:NM_008866 - - NM_008866 - - chr1:4807892-4846735 - - 15.4661 12.8039 18.1283 OK
../Nsg3-Hip_tophat/cufflinks_output_gtf/genes.fpkm_tracking:NM_008866 - - NM_008866 - - chr1:4807892-4846735 - - 13.0078 10.6329 15.3827 OK

Here the aggregete value of 18.3 is larger than the individual values 16.1, 15.5, and 13.0. How does cuffdiff calculate the aggregate values from the 3 samples?
Does it normalize? How does it do so?

I've tried finding this in the Trapnell, 2012 Nature Protocol paper, but it doesn't say.

Thanks, csmatyi
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