Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Cuffdiff results; no replicates ccard28 Bioinformatics 5 02-20-2014 12:38 PM
Cuffdiff vastly different results jfreimer Bioinformatics 1 08-15-2013 11:57 PM
Cuffdiff Results confidence help himanshu04 Bioinformatics 6 05-10-2013 04:53 AM
Cuffdiff - results replicates adrian Bioinformatics 4 02-24-2013 05:04 PM
Suspicious results from CuffDiff Pejman Bioinformatics 1 02-20-2011 02:20 PM

Thread Tools
Old 08-26-2015, 03:13 PM   #1
Location: San Francisco, CA

Join Date: Aug 2011
Posts: 91
Question cuffdiff results

Looking at some publicly available RNAseq data. I ran cuffdiff on a pair of tumor-normal RNAseq data downloaded from TCGA, and I'm wondering what those results mean.

In the gene_exp.diff or the genes.fpkm_tracking file, if I add up all the FPKM values for both samples, one of the sums is 2.6 times as large as the other sum.
If I add up all the counts for both samples, one of the sums is 0.86 times as large as the other sum.

Why is there such a large difference in FPKM when read counts are comparable? You may say, well all the reads in one sample get mapped to large genes in one sample but small genes in the other sample..... but what does that imply?

lethalfang is offline   Reply With Quote

cuffdiff, fpkm, rnaseq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:37 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO